bluuebunny/crossref_metadata_2025 huggingface dataset:
Effective results for unit equations over finitely generated integral domains
Authors: EVERTSE JAN–HENDRIK , GYŐRY KÁLMÁN
Published: November 2012

LetA⊃ ℤ be an integral domain which is finitely generated over ℤ and leta,b,cbe non-zero elements ofA. Extending earlier work of Siegel, Mahler and Parry, in 1960 Lang proved that the equation (*)aϵ +bη =cin ϵ, η ∈A* has only finitely many solutions. Using Baker's theory of logarithmic forms, Győry proved, in 1979, that the solutions of (*) can be determined effectively ifAis contained in an algebraic number field. In this paper we prove, in a quantitative form, an effective finiteness result for equations (*) over an arbitrary integral domainAof characteristic 0 which is finitely generated over ℤ. Our main tools are already existing effective finiteness results for (*) over number fields and function fields, an effective specialization argument developed by Győry in the 1980's, effective results of Hermann (1926) and Seidenberg (1974) on linear equations over polynomial rings over fields, and similar such results by Aschenbrenner, from 2004, on linear equations over polynomial rings over ℤ. We prove also an effective result for the exponential equationaγ1v1···γsvs+bγ1w1··· γsws=cin integersv1,…,ws, wherea,b,cand γ1,…,γsare non-zero elements ofA.
Risk ofStaphylococcus aureuscarriage in childcare employees
Authors: MORITZ E. D. , SMITH T. C.
Published: November 2012

Asymptomatic carriage ofStaphylococcus aureusis an important risk factor for developing infection, as well as a key contributor to transmission. Despite the fact that childcare workers are at known risk for infections, little research has focused on bacterial carriage in this occupational group. We conducted a cross-sectional study comparing the prevalence ofS. aureusin 110 childcare employees with the prevalence in 111 unexposed participants. Questionnaire data was collected for employees, unexposed adults, and children. Multivariate analysis allowed for adjustment for confounders. Data on work-related exposures are presented as well. The prevalence ofS. aureusin employees, unexposed adults, children, and on surfaces was 35·2%, 33·6%, 19·8%, and 9·8%, respectively. Washing children's hands upon their arrival at childcare facilities may decrease the risk ofS. aureuscarriage in employees (odds ratio 0·17, 95% confidence interval 0·095–0·32,P < 0·0001).
Grammatical relation probability: How usage patterns shape analogy
Authors: Brown Esther L. , Rivas Javier
Published: November 2012

It has been argued speakers' knowledge of the probabilities of certain phones, words, and syntactic structures affects language production (Bell, Brenier, Gregory, Girand, & Jurafsky, 2009; Tily, Gahl, Arnon, Snider, Kothari, & Bresnan, 2009). This study provides evidence for effects of grammatical relation probabilities by identifying significant effects on verb morphology in the Spanish presentative [haber‘there (be)’+ NP] construction stemming from nouns with varying proportion of use in subject function. In addition to this novel type of probability (grammatical relation), we present calculations that are not context-dependent but cumulative, reflecting speakers' overall experience with these nouns in the grammar. We conduct variationist analyses on corpora of spoken Puerto Rican Spanish. Our results reveal that nouns with a high probability of subject function promote the analogical leveling ofhaberby increasing the likelihood of reanalysis of the object as subject of the construction. We interpret these results as suggesting speakers possess lexicalized knowledge of grammatical relation usage patterns.
Nutrition and the HIV-associated lipodystrophy syndrome
Authors: Loonam Cathríona Rosemary , Mullen Anne
Published: November 2012

HIV-associated lipodystrophy syndrome (HALS), comprising metabolic and morphological alterations, is a known side effect of highly active antiretroviral therapy (HAART). Evidence for the role of nutrition in the management of the systemic parameters of HALS is currently limited. In the present paper we review the current knowledge base surrounding HALS, focusing particularly on the role of nutrition in mitigating the systemic parameters of the syndrome. Reported prevalence of HALS was found to vary from 9 to 83 % due to lack of a standardised definition, as well as variations in assessment methods and in the study population used. HALS is associated with both morphological (lipoatrophy, lipohypertrophy) and metabolic (dyslipidaemia, glucose intolerance, diabetes, hypertension, endothelial dysfunction and atherosclerosis) alterations, which may occur singly or in combination, and are associated with an increased risk of CVD. HAART-induced adipocyte inflammation, oxidative stress and macrophage infiltration, as well as altered adipocyte function and mitochondrial toxicity, have been shown to be central to the development of HALS. The adipocyte, therefore, represents a plausible target for treatment. Pharmacological and surgical treatment interventions have shown effect. However, their use is associated with numerous adverse effects and complications. Targeted lifestyle interventions may provide a useful alternative for managing HALS owing to their safety and tolerability. A Mediterranean-style diet has been found to be effective in improving the systemic parameters of HALS. Furthermore, the effects ofn-3 PUFA supplementation are encouraging and future randomised controlled trials investigating the beneficial effects ofn-3 PUFA in HALS are justified.
Peripheral signalling involved in energy homeostasis control
Authors: Lancha Andoni , Frühbeck Gema , Gómez-Ambrosi Javier
Published: November 2012

The alarming prevalence of obesity has led to a better understanding of the molecular mechanisms controlling energy homeostasis. Regulation of energy intake and expenditure is more complex than previously thought, being influenced by signals from many peripheral tissues. In this sense, a wide variety of peripheral signals derived from different organs contributes to the regulation of body weight and energy expenditure. Besides the well-known role of insulin and adipokines, such as leptin and adiponectin, in the regulation of energy homeostasis, signals from other tissues not previously thought to play a role in body weight regulation have emerged in recent years. The role of fibroblast growth factor 21 (FGF21), insulin-like growth factor 1 (IGF-I), and sex hormone-binding globulin (SHBG) produced by the liver in the regulation of body weight and insulin sensitivity has been recently described. Moreover, molecules expressed by skeletal muscle such as myostatin have also been involved in adipose tissue regulation. Better known is the involvement of ghrelin, cholecystokinin, glucagon-like peptide 1 (GLP-1) and PYY3–36, produced by the gut, in energy homeostasis. Even the kidney, through the production of renin, appears to regulate body weight, with mice lacking this hormone exhibiting resistance to diet-induced obesity. In addition, the skeleton has recently emerged as an endocrine organ, with effects on body weight control and glucose homeostasis through the actions of bone-derived factors such as osteocalcin and osteopontin. The comprehension of these signals will help in a better understanding of the aetiopathology of obesity, contributing to the potential development of new therapeutic targets aimed at tackling excess body fat accumulation.
Microbial Diversity and Biogeochemical Function of the Phototrophic Microbial Mats of Epsomitic Hot Lake, WA
Authors: Lindemann S.R. , Moran J.J. , Dohnalkova A. , Kim Y. , Kennedy D.W. , Stolyar S. , Majors P.D. , Wiley H. , Konopka A.E. , Fredrickson J.K.
Published: November 2012

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.
Imaging and Analysis of Microbially Induced Calcium Carbonate Precipitates and Biofilm at the Center for Biofilm Engineering, Montana State University
Authors: Connolly J. , Pitts B. , Cunningham A. , Gerlach R.
Published: November 2012

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.
Focusing in on Microbial Biofilms with Advanced Imaging and Genomic Approaches
Authors: McLean J.S.
Published: November 2012

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.
Understanding the Relationships Among Substrate, Medium, and Biofilm Physiology through Microscopic Approaches
Authors: Hurtubise J.M. , Schlosser R.W. , Mirau P.A. , Goodson W.J. , Lloyd P.F. , Kay M.L. , Knight C.L.
Published: November 2012

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.
Nano-FTIR chemical mapping of minerals in biological materials
Authors: Amarie S. , Keilmann F. , Zaslansky P. , Griesshaber E. , Schmahl W. , Kajihara Y.
Published: November 2012

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.
Analytical Techniques for Characterizing Defects and Morphology of Polymer Films
Authors: Kodjie S. , Guerra S. , Nilesh S.
Published: November 2012

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.
Interplay of Influenza Hemagglutinin and Membranes During Fusion
Authors: Lee K.K. , Gui L. , Ebner J.
Published: November 2012

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.
Structure Of The Mitochondrial ATP Synthase And Its Role In Shaping Mitochondria Cristae
Authors: Davies K.M. , Daum B. , Kühlbrandt W. , Anselmi C. , Faraldo-Gómez J.
Published: November 2012

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.
Surface for catalysis by poliovirus RNA dependent RNA polymerase
Authors: Wang J. , Bullitt E. , Kirkegaard K.
Published: November 2012

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.
Design and characterization of 50 kW solid-state RF amplifier
Authors: Jain Akhilesh , Hannurkar P. R. , Sharma D. K. , Gupta A. K. , Tiwari A. K. , Lad M. , Kumar R. , Gupta P. D. , Pathak S. K.
Published: November 2012

Radio frequency (RF) and microwave amplifier research has been largely focused on solid-state technology in recent years. This paper presents design and performance characterization of a 50-kW modular solid-state amplifier, operating at 505.8 MHz. It includes architecture selection and design procedures based on circuit and EM simulations for its building blocks like solid-state amplifier modules, combiners, dividers, and directional couplers. Key performance objectives such as efficiency, return loss, and amplitude/phase imbalance are discussed for this amplifier for real-time operation. This amplifier is serving as the state-of-the-art RF source in Indus-2 synchrotron radiation source. Characterization on component level as well as system level of this amplifier serves useful data for RF designers working in communication and particle accelerator fields.
Association between infant nutrition and anthropometry, and pre-pubertal body composition in urban South African children
Authors: Kagura J. , Feeley A. B. B. , Micklesfield L. K. , Pettifor J. M. , Norris S. A.
Published: November 2012

Early life nutrition and growth are related to subsequent obesity risk in high-income countries. We investigated the association between nutrition and growth during infancy, and body composition at 10 years of age in 140 children selected from the Bone Health sub-study of the Birth-to-Twenty cohort from Soweto, Johannesburg, South Africa. Infant feeding and dietary data were collected during the first 12 months, and weight and height were measured at 1 and 2 years of age. At 10 years, anthropometry and dual-energy X-ray absorptiometry (DXA)-derived body composition were measured. Regression models were used to determine associations between independent and dependent variables at the 1% level of significance. A one z-score increase in birth weight was associated with a 1051 g increase in lean mass and a 0.22 increase in body mass index (BMI) z-score at the age of 10 years. After adjusting for confounders, stunting at age 1 year was associated with lower fat mass only at 10 years of age while at age 2 years, it was associated with lower lean mass only. Being underweight at one year of age was significantly associated with lower lean mass only. Weight-for-age (WAZ) change in the second year of infancy was a predictor of fat mass and BMI only. Body fatness at 10 years of age was positively associated with infant WAZ change rather than height-for-age change. There were no significant associations between infant dietary patterns, wasting and being underweight at age 2 years and pre-pubertal body composition. Further studies are needed to assess whether these associations continue during adolescence as pubertal development may be an important modifier of these associations.
What kind of interaction receives high and low ratings in Oral Proficiency Interviews?
Authors: Seedhouse Paul
Published: November 2012

Based on a Conversation Analysis (CA) of a corpus of Oral Proficiency Interviews (OPI), the study asks what kind of interaction receives high and low ratings in OPIs. The discussion focuses on issues of interactional organisation, considering turn-taking, sequence, repair and topic development in relation to candidate scores. The study presents findings of two funded studies of the International English Language Testing System (IELTS) Speaking Test (IST), which is one part of IELTS, a major international English proficiency test.

The article explains how interaction in the IST is organised in interactional terms and how this organisation generates opportunities to differentiate high- and low-scoring interaction. The study then lists the interactional characteristics of high-scoring and low-scoring tests, based on an inductive search through the database and analysis of the micro-interaction. Extracts are presented to support characterisations. Differences in score correlate to the following interactional differences in Parts 1 and 3 of the IST: ability to answer the question, engage with and develop a topic coherently, amount of trouble and repair, lexical choice, and identity construction. In Part 2 of the IST, length of turn may also be related to score.
Aiming high, but investing little
Authors: Meyer Morgan
Published: November 2012

The French government has ambitious goals to make France a leading nation for synthetic biology research, but it still needs to put its money where its mouth is and provide the field with dedicated funding and other support.
On the road to improve the bioremediation and electricity-harvesting skills of Geobacter sulfurreducens: functional and structural characterization of multihaem cytochromes
Authors: Morgado Leonor , Fernandes Ana P. , Dantas Joana M. , Silva Marta A. , Salgueiro Carlos A.
Published: November 2012

Extracellular electron transfer is one of the physiological hallmarks of Geobacter sulfurreducens, allowing these bacteria to reduce toxic and/or radioactive metals and grow on electrode surfaces. Aiming to functionally optimize the respiratory electron-transfer chains, such properties can be explored through genetically engineered strains. Geobacter species comprise a large number of different multihaem c-type cytochromes involved in the extracellular electron-transfer pathways. The functional characterization of multihaem proteins is particularly complex because of the coexistence of several microstates in solution, connecting the fully reduced and oxidized states. NMR spectroscopy has been used to monitor the stepwise oxidation of each individual haem and thus to obtain information on each microstate. For the structural study of these proteins, a cost-effective isotopic labelling of the protein polypeptide chains was combined with the comparative analysis of 1H-13C HSQC (heteronuclear single-quantum correlation) NMR spectra obtained for labelled and unlabelled samples. These new methodological approaches allowed us to study G. sulfurreducens haem proteins functionally and structurally, revealing functional mechanisms and key residues involved in their electron-transfer capabilities. Such advances can now be applied to the design of engineered haem proteins to improve the bioremediation and electricity-harvesting skills of G. sulfurreducens.
Rates and potential mechanism of anaerobic nitrate-dependent microbial pyrite oxidation
Authors: Bosch Julian , Meckenstock Rainer U.
Published: November 2012

Pyrite (FeS2) is a major iron- and sulfur-containing mineral phase in the environment. Oxidation of pyrite by aerobic micro-organisms has been well investigated. However, the reactivity of pyrite under anoxic conditions is still an open question. In the present paper, we summarize field and laboratory data on this chemolithotrophic respiration process with nitrate as terminal electron acceptor. Geochemical and stable isotope field data indicate that this process is occurring. Laboratory studies are more ambiguous, but recent positive results provide evidence that anaerobic microbial pyrite oxidation can, in fact, occur with nitrate as electron acceptor.
Operational and technical considerations for microbial electrosynthesis
Authors: Desloover Joachim , Arends Jan B.A. , Hennebel Tom , Rabaey Korneel
Published: November 2012

Extracellular electron transfer has, in one decade, emerged from an environmental phenomenon to an industrial process driver. On the one hand, electron transfer towards anodes leads to production of power or chemicals such as hydrogen, caustic soda and hydrogen peroxide. On the other hand, electron transfer from cathodes enables bioremediation and bioproduction. Although the microbiology of extracellular electron transfer is increasingly being understood, bringing the processes to application requires a number of considerations that are both operational and technical. In the present paper, we investigate the key applied aspects related to electricity-driven bioproduction, including biofilm development, reactor and electrode design, substrate fluxes, surface chemistry, hydrodynamics and electrochemistry, and finally end-product removal/toxicity. Each of these aspects will be critical for the full exploitation of the intriguing physiological feat that extracellular electron transfer is today.
Does bioelectrochemical cell configuration and anode potential affect biofilm response?
Authors: Kumar Amit , Katuri Krishna , Lens Piet , Leech Dónal
Published: November 2012

Electrochemical gradients are the backbone of basic cellular functions, including chemo-osmotic transport and ATP synthesis. Microbial growth, terminal respiratory proteins and external electron transfer are major pathways competing for electrons. In BESs (bioelectrochemical systems), such as MFCs (microbial fuel cells), the electron flow can be via soluble inorganic/organic molecules or to a solid surface. The flow of electrons towards a solid surface can be via outer-membrane cytochromes or electron-shuttle molecules, mediated by conductive protein nanowires or extracellular matrices. In MECs (microbial electrolysis cells), the anode potential can vary over a wide range, which alters the thermodynamic energy available for bacteria capable of donating electrons to the electrode [termed EAB (electroactive bacteria)]. Thus the anode potential is an important electrochemical parameter determining the growth, electron distribution/transfer and electrical activity of films of these bacteria on electrodes. Different optimal applied potentials to anodes have been suggested in the literature, for selection for microbial growth, diversity and performance in biofilms on electrodes. In the present paper, we review the effects of anode potentials on electron-transfer properties of such biofilms, and report on the effect that electrochemical cell configuration may have on performance.
Analysis of structural MtrC models based on homology with the crystal structure of MtrF
Authors: Edwards Marcus J. , Fredrickson James K. , Zachara John M. , Richardson David J. , Clarke Thomas A.
Published: November 2012

The outer-membrane decahaem cytochrome MtrC is part of the transmembrane MtrCAB complex required for mineral respiration by Shewanella oneidensis. MtrC has significant sequence similarity to the paralogous decahaem cytochrome MtrF, which has been structurally solved through X-ray crystallography. This now allows for homology-based models of MtrC to be generated. The structure of these MtrC homology models contain ten bis-histidine-co-ordinated c-type haems arranged in a staggered cross through a four-domain structure. This model is consistent with current spectroscopic data and shows that the areas around haem 5 and haem 10, at the termini of an octahaem chain, are likely to have functions similar to those of the corresponding haems in MtrF. The electrostatic surfaces around haem 7, close to the β-barrels, are different in MtrF and MtrC, indicating that these haems may have different potentials and interact with substrates differently.
Biogeochemistry and microbiology of microaerobic Fe(II) oxidation
Authors: Emerson David
Published: November 2012

Today high Fe(II) environments are relegated to oxic–anoxic habitats with opposing gradients of O2 and Fe(II); however, during the late Archaean and early Proterozoic eons, atmospheric O2 concentrations were much lower and aqueous Fe(II) concentrations were significantly higher. In current Fe(II)-rich environments, such as hydrothermal vents, mudflats, freshwater wetlands or the rhizosphere, rusty mat-like deposits are common. The presence of abundant biogenic microtubular or filamentous iron oxyhydroxides readily reveals the role of FeOB (iron-oxidizing bacteria) in iron mat formation. Cultivation and cultivation-independent techniques, confirm that FeOB are abundant in these mats. Despite remarkable similarities in morphological characteristics between marine and freshwater FeOB communities, the resident populations of FeOB are phylogenetically distinct, with marine populations related to the class Zetaproteobacteria, whereas freshwater populations are dominated by members of the Gallionallaceae, a family within the Betaproteobacteria. Little is known about the mechanism of how FeOB acquire electrons from Fe(II), although it is assumed that it involves electron transfer from the site of iron oxidation at the cell surface to the cytoplasmic membrane. Comparative genomics between freshwater and marine strains reveals few shared genes, except for a suite of genes that include a class of molybdopterin oxidoreductase that could be involved in iron oxidation via extracellular electron transport. Other genes are implicated as well, and the overall genomic analysis reveals a group of organisms exquisitely adapted for growth on iron.
Influence of Fe2+-catalysed iron oxide recrystallization on metal cycling
Authors: Latta Drew E. , Gorski Christopher A. , Scherer Michelle M.
Published: November 2012

Recent work has indicated that iron (oxyhydr-)oxides are capable of structurally incorporating and releasing metals and nutrients as a result of Fe2+-induced iron oxide recrystallization. In the present paper, we briefly review the current literature examining the mechanisms by which iron oxides recrystallize and summarize how recrystallization affects metal incorporation and release. We also provide new experimental evidence for the Fe2+-induced release of structural manganese from manganese-doped goethite. Currently, the exact mechanism(s) for Fe2+-induced recrystallization remain elusive, although they are likely to be both oxide-and metal-dependent. We conclude by discussing some future research directions for Fe2+-catalysed iron oxide recrystallization.
The role of Rab GTPases in the transport of vacuoles containingLegionella pneumophilaandCoxiella burnetii
Authors: Hardiman Camille A. , McDonough Justin A. , Newton Hayley J. , Roy Craig R.
Published: November 2012

Intracellular pathogens survive in eukaryotic cells by evading a variety of host defences. To avoid degradation through the endocytic pathway, intracellular bacteria must adapt their phagosomes into protective compartments that promote bacterial replication. Legionella pneumophila and Coxiella burnetii are Gram-negative intracellular pathogens that remodel their phagosomes by co-opting components of the host cell, including Rab GTPases. L. pneumophila and C. burnetii are related phylogenetically and share an analogous type IV secretion system for delivering bacterial effectors into the host cell. Some of these effectors mimic eukaryotic biochemical activities to recruit and modify Rabs at the vacuole. In the present review, we cover how these bacterial species, which utilize divergent strategies to establish replicative vacuoles, use translocated proteins to manipulate host Rabs, as well as exploring which Rabs are implicated in vacuolar biogenesis in these two organisms.
Regulating colicin synthesis to cope with stress and lethality of colicin production
Authors: Žgur-Bertok Darja
Published: November 2012

Colicins are plasmid-encoded bacteriocins active against Escherichia coli and closely related species of Enterobacteriaceae. They promote microbial diversity and genetic diversity in E. coli populations. Colicin synthesis is characteristically repressed by the LexA protein, the key regulator of the SOS response. As colicins are released by cell lysis, generally two LexA dimers binding to two overlapping SOS boxes control untimely expression. Nevertheless, genetic organization of the colicin clusters, additional transcription regulators as well as post-transcriptional mechanisms involving translational efficiency of the lysis and activity genes fine-tune colicin expression and protect against lethality of colicin production.
Translocation trumps receptor binding in colicin entry into Escherichia coli
Authors: Jakes Karen S.
Published: November 2012

Of the steps involved in the killing of Escherichia coli by colicins, binding to a specific outer-membrane receptor was the best understood and earliest characterized. Receptor binding was believed to be an indispensable step in colicin intoxication, coming before the less well-understood step of translocation across the outer membrane to present the killing domain to its target. In the process of identifying the translocator for colicin Ia, I created chimaeric colicins, as well as a deletion missing the entire receptor-binding domain of colicin Ia. The normal pathway for colicin Ia killing was shown to require two copies of Cir: one that serves as the primary receptor and a second copy that serves as translocator. The novel Ia colicins retain the ability to kill E. coli, even in the absence of receptor binding, as long as they can translocate via their Cir translocator. Experiments to determine whether colicin M uses a second copy of its receptor, FhuA, as its translocator were hampered by precipitation of colicin M chimaeras in inclusion bodies. Nevertheless, I show that receptor binding can be bypassed for killing, as long as a translocation pathway is maintained for colicin M. These experiments suggest that colicin M, unlike colicin Ia, may normally use a single copy of FhuA as both its receptor and its translocator. Colicin E1 can kill in the absence of receptor binding, using translocation through TolC.
Colicin A binds to a novel binding site of TolA in the Escherichia coli periplasm
Authors: Penfold Christopher N. , Li Chan , Zhang Ying , Vankemmelbeke Mireille , James Richard
Published: November 2012

Colicins are protein antibiotics produced by Escherichia coli to kill closely related non-identical competing species. They have taken advantage of the promiscuity of several proteins in the cell envelope for entry into the bacterial cell. The Tol–Pal system comprises one such ensemble of periplasmic and membrane-associated interacting proteins that links the IM (inner membrane) and OM (outer membrane) and provides the cell with a structural scaffold for cell division and energy transduction. Central to the Tol–Pal system is the TolA hub protein which forms protein–protein interactions with all other members and also with extrinsic proteins such as colicins A, E1, E2–E9 and N, and the coat proteins of the Ff family of filamentous bacteriophages. In the present paper, we review the role of TolA in the translocation of colicin A through the recently determined crystal structure of the complex of TolA with a translocation domain peptide of ColA (TA53–107), we demonstrate that TA53–107 binds to TolA at a novel binding site and compare the interactions of TolA with other colicins that use the Tol–Pal system for cell entry substantiating further the role of TolA as a periplasmic hub protein.
How Bugs Kill Bugs: Progress and Challenges in Bacteriocin Research
Authors: Penfold Christopher N. , Walker Daniel , Kleanthous Colin
Published: November 2012

A Biochemical Society Focused Meeting on bacteriocins was held at the University of Nottingham on 16–18 July 2012 to mark the retirement of Professor Richard James and honour a scientific career of more than 30 years devoted to an understanding of the biology of colicins, bacteriocins produced by Escherichia coli. This meeting was the third leg of a triumvirate of symposia that included meetings at the Île de Bendor, France, in 1991 and the University of East Anglia, Norwich, U.K., in 1998, focused on bringing together leading experts in basic and applied bacteriocin research. The symposium which attracted 70 attendees consisted of 18 invited speakers and 22 selected oral communications spread over four themes: (i) Role of bacteriocins in bacterial ecology, (ii) Mode of action of bacteriocins, (ii) Mechanisms of bacteriocin import across the cell envelope, and (iv) Biotechnological and biomedical applications of bacteriocins. Speakers and poster presenters travelled from around the world, including the U.S.A., Japan, Asia and Europe, to showcase the latest developments in their scientific research.
Colicin translocation across the Escherichia coli outer membrane
Authors: Housden Nicholas G. , Kleanthous Colin
Published: November 2012

We are investigating how protein bacteriocins import their toxic payload across the Gram-negative cell envelope, both as a means of understanding the translocation process itself and as a means of probing the organization of the cell envelope and the function of the protein machines within it. Our work focuses on the import mechanism of the group A endonuclease (DNase) colicin ColE9 into Escherichia coli, where we combine in vivo observations with structural, biochemical and biophysical approaches to dissect the molecular mechanism of colicin entry. ColE9 assembles a multiprotein ‘translocon’ complex at the E. coli outer membrane that triggers entry of the toxin across the outer membrane and the simultaneous jettisoning of its tightly bound immunity protein, Im9, in a step that is dependent on the protonmotive force. In the present paper, we focus on recent work where we have uncovered how ColE9 assembles its translocon complex, including isolation of the complex, and how this leads to subversion of a signal intrinsic to the Tol–Pal assembly within the periplasm and inner membrane. In this way, the externally located ColE9 is able to ‘connect’ to the inner membrane protonmotive force via a network of protein–protein interactions that spans the entirety of the E. coli cell envelope to drive dissociation of Im9 and initiate entry of the colicin into the cell.
Can elevated CO2 combined with high temperature ameliorate the effect of terminal drought in wheat?
Authors: Dias de Oliveira Eduardo , Bramley Helen , Siddique Kadambot H. M. , Henty Samuel , Berger Jens , Palta Jairo A.
Published: November 2012

Wheat (Triticum aestivum L.) production may be affected by the future climate, but the impact of the combined increases in atmospheric CO2 concentration, temperature and incidence of drought that are predicted has not been evaluated. The combined effect of elevated CO2, high temperature and terminal drought on biomass accumulation and grain yield was evaluated in vigorous (38–19) and nonvigorous (Janz) wheat genotypes grown under elevated CO2 (700 µL L–1) combined with temperatures 2°C, 4°C and 6°C above the current ambient temperature. Terminal drought was induced in all combinations at anthesis in a split-plot design to test whether the effect of elevated CO2 combined with high temperature ameliorates the negative effects of terminal drought on biomass accumulation and grain yield. Biomass and grain yield were enhanced under elevated CO2 with 2°C above the ambient temperature, regardless of the watering regimen. The combinations of elevated CO2 plus 4°C or 6°C above the ambient temperature did not enhance biomass and grain yield, but tended to decrease them. The reductions in biomass and grain yield (45–50%) caused by terminal drought were less severe (21–28%) under elevated CO2 with 2°C above the ambient temperature. The amelioration resulted from a 63% increase in the rate of leaf net photosynthesis in 38–19 and a 39% increase in tillering and leaf area in Janz. The contrasting responses and phenological development of these two genotypes to the combination of elevated CO2, temperature and terminal drought, and the possible influences on their source–sink relationships are discussed.
Dissecting the mechanism of abscisic acid-induced dynamic microtubule reorientation using live cell imaging
Authors: Seung David , Webster Michael W. , Wang Richard , Andreeva Zornitza , Marc Jan
Published: November 2012

Abscisic acid (ABA) is involved in plant development and responses to environmental stress including the formation of longitudinal microtubule arrays in elongating cells, although the underlying mechanism for this is unknown. We explored ABA-induced microtubule reorientation in leek (Allium porrum L.) leaf epidermal cells transiently expressing a GFP–MBD microtubule reporter. After 14–18 h incubation with ABA, the frequency of cells with longitudinal arrays of cortical microtubules along the outer epidermal wall increased with dose-dependency until saturation at 20 μM. Time-course imaging of individual cells revealed a gradual increase in the occurrence of discordant, dynamic microtubules deviating from the normal transverse microtubule array within 2–4 h of exposure to ABA, followed by reorientation into a completely longitudinal array within 5–8 h. Approximately one-half of the ABA-induced reorientation occurred independently of cytoplasmic streaming following the application of cytochalasin D. Reorientation occurred also in the elongation zone of Arabidopsis root tips. Transient expression of AtEB1b–GFP reporter and analysis of ‘comet’ velocities in Allium revealed that the microtubule growth rate increased by 55% within 3 h of exposure to ABA. ABA also increased the sensitivity of microtubules to depolymerisation by oryzalin and exacerbated oryzalin-induced radial swelling of Arabidopsis root tips. The swelling was further aggravated in AtPLDδ-null mutant, suggesting PLDδ plays a role in microtubule stability. We propose that ABA-induced reorientation of transverse microtubule array initially involves destabilisation of the array combined with the formation of dynamic, discordant microtubules.
Assessing the effect of foliar moisture on the spread rate of crown fires
Authors: Alexander Martin E. , Cruz Miguel G.
Published: November 2012

This paper constitutes a digest and critique of the currently available information pertaining to the influence of live fuel or foliar moisture content (FMC) on the spread rate of crown fires in conifer forests and shrublands. We review and discuss the findings from laboratory experiments and field-based fire behaviour studies. Laboratory experimentation with single needles or leaves and small conifer trees has shown an unequivocal effect of FMC on flammability metrics. A much less discernible effect of FMC on crown fire rate of spread was found in the existing set of experimental crown fires carried out in conifer forests and similarly with the far more robust database of experimental fires conducted in shrubland fuel complexes. The high convective and radiant heat fluxes associated with these fires and the lack of appropriate experimental design may have served to mask any effect of FMC or live fuel moisture on the resulting spread rate. Four theoretical functions and one empirical function used to adjust rate of fire spread for the effect of foliar or live fuel moisture were also concurrently examined for their validity over a wide range of FMC conditions with varying outcomes and relevancy. None of these model functions was found suitable for use with respect to dead canopy foliage.
Structural mechanism of ubiquitin and NEDD8 deamidation catalyzed by bacterial effectors that induce macrophage-specific apoptosis
Authors: Yao Qing , Cui Jixin , Wang Jiayi , Li Ting , Wan Xiaobo , Luo Tianming , Gong Yi-Nan , Xu Ying , Huang Niu , Shao Feng
Published: November 2012

Targeting eukaryotic proteins for deamidation modification is increasingly appreciated as a general bacterial virulence mechanism. Here, we present an atomic view of how a bacterial deamidase effector, cycle-inhibiting factor homolog in
Burkholderia pseudomallei
(CHBP), recognizes its host targets, ubiquitin (Ub) and Ub-like neural precursor cell expressed, developmentally down-regulated 8 (NEDD8), and catalyzes site-specific deamidation. Crystal structures of CHBP–Ub/NEDD8 complexes show that Ub and NEDD8 are similarly cradled by a large cleft in CHBP with four contacting surfaces. The pattern of Ub/NEDD8 recognition by CHBP resembles that by the E1 activation enzyme, which critically involves the Lys-11 surface in Ub/NEDD8. Close examination of the papain-like catalytic center reveals structural determinants of CHBP being an obligate glutamine deamidase. Molecular-dynamics simulation identifies Gln-31/Glu-31 of Ub/NEDD8 as one key determinant of CHBP substrate preference for NEDD8. Inspired by the idea of using the unique bacterial activity as a tool, we further discover that CHBP-catalyzed NEDD8 deamidation triggers macrophage-specific apoptosis, which predicts a previously unknown macrophage-specific proapoptotic signal that is negatively regulated by neddylation-mediated protein ubiquitination/degradation.
The agencies method for coalition formation in experimental games
Authors: Nash John F. , Nagel Rosemarie , Ockenfels Axel , Selten Reinhard
Published: November 2012

In society, power is often transferred to another person or group. A previous work studied the evolution of cooperation among robot players through a coalition formation game with a non-cooperative procedure of acceptance of an agency of another player. Motivated by this previous work, we conduct a laboratory experiment on finitely repeated three-person coalition formation games. Human players with different strength according to the coalition payoffs can accept a transfer of power to another player, the agent, who then distributes the coalition payoffs. We find that the agencies method for coalition formation is quite successful in promoting efficiency. However, the agent faces a tension between short-term incentives of not equally distributing the coalition payoff and the long-term concern to keep cooperation going. In a given round, the strong player in our experiment often resolves this tension approximately in line with the Shapley value and the nucleolus. Yet aggregated over all rounds, the payoff differences between players are rather small, and the equal division of payoffs predicts about 80% of all groups best. One reason is that the voting procedure appears to induce a balance of power, independent of the individual player's strength: Selfish subjects tend to be voted out of their agency and are further disciplined by reciprocal behaviors.
Minimalist metaphors
Authors: Sweetser Eve , Sullivan Karen
Published: November 2012

We suggest that the impact of metaphoric language does not depend entirely on the conceptual metaphor that is evoked, nor on the form the metaphoric language takes, but also on the steps involved in evoking a given metaphor. This is especially apparent in minimalist poetry. Readers are given hints, cultural conventions, or no guidance at all, on how to fill in missing metaphoric domains and mappings. We place minimalist metaphors at the “effortful” end of the cline proposed by Stockwell (1992), and suggest that the other end can be associated with maximalist metaphors, which corral the reader into a highly specific interpretation. The degree of minimalism or maximalism depends on the specific mappings that are linguistically indicated, the degree of conventionalization of the metaphor, and reliance on cultural background knowledge.
Mind the gap!
Authors: Laporte Samantha
Published: November 2012

A paradigm gap has long separated the fields of World Englishes and Learner Englishes: they have mainly been dealt with separately and very little consideration has been given to the features that they might share. Recently, however, Nesselhauf (2009) has highlighted that some features thought to be variety-specific are in fact shared by World and Learner varieties. This paper examines their use of the high-frequency verb make in samples of corpora of student writing of four World Englishes, four Learner Englishes and a control corpus of English as a Native Language (ENL). This case study shows that, quantitatively, the World and Learner varieties are mainly characterized by heterogeneity, while qualitatively, a number of similarities distinguish them from ENL.
J. S. Mill on Poetry and Rhetoric
Authors: Whedbee Karen E.
Published: November 2012

In his essay “What is Poetry ?”(1833), John Stuart Mill described the difference between rhetoric and poetry using the antithesis, “rhetoric is heard; poetry is overheard.” In the twentieth century, scholars from the field of Speech Communication appropriated Mill's words as justification for the separation of Speech Communication (and rhetorical criticism) from English (and literary criticism). This essay argues that twentieth-century scholars misunderstood Mill's meaning. They failed to recognize that, for Mill, the key issue was not the frequently quoted distinction between rhetoric and poetry but a more problematic distinction between art and science.
“Speech is a Powerful Lord”: Speech, Sound, and Enchantment in Greek Oratorical Performance
Authors: Johnstone Christopher Lyle
Published: November 2012

The performative dimension of oral rhetoric has been a central concern of theorists throughout the history of the tradition. Awareness of the persuasive power of the human voice is especially conspicuous in the teachings of Gorgias of Leontini. When he claims that “speech is a powerful lord,” Gorgias articulates a profound insight into how the human mind and body respond to sounds produced by the voice. By examining Gorgias' views of the potency of speech in the context of the oral, poetic tradition of ancient Greece, we can appreciate more fully the sources of this insight. Moreover, contemporary research in psycho-physiology suggests that Gorgias grasped an important dimension of the human mind's fundamental nature.
Style, Character, and Persuasion in Aristotle's Rhetoric
Authors: Bruss Kristine , Graff Richard
Published: November 2012

Aristotle's Rhetoric leaves a number of unanswered questions, among them the nature of the relationship between verbal style and êthos, or character, as a means of persuasion. Statements throughout the Rhetoric suggest a connection between manner of expression and persuasive character, but Aristotle's ideas in this area are underdeveloped. Here we argue that Aristotle's stylistic theory, while not demonstrably inconsistent with the technical proof through character, cannot be made to conform neatly with it in most salient respects. Though Aristotle does not explicit y identify style as a means through which the speaker may convey the impression that he possesses positive intellectual or moral qualities, he does recognize a role for lexis in the expression of generic character traits and is aware that an inappropriate style will damage the speaker's credibility. Hence, attention to style is important for the presentation of a plausible êthos and, in this limited respect, style does contribute to the maintenance of persuasive character. This conclusion must be inferred from passing remarks in the Rhetoric. The absence of a more fully developed theory is curious in light of the availability of examples from the discourse of Attic logographers like Lysias, a speechwriter universally praised by later critics for his mastery of ethopoeia(character portrayal).
Acting Up: Drama and the Rhetorical Education of Progressive-Era Teachers at Three Massachusetts State Normal Schools
Authors: Rothermel Beth Ann
Published: November 2012

This essay considers the diverse pedagogical purposes the study of drama served in the rhetorical preparation of teachers at three progressive-era normal schools for women, the Framingham, Westfield, and Salem State Normal Schools. Drawing on scholarship and archival materials, I argue that these normal schools both introduced future teachers to drama as a tool to help their pupils learn and employed dramatic activity as a means to prepare future teachers for their lives in the classroom. Through work in drama, future teachers made explicit connections between learning and playmaking, pedagogy and theatrics, teaching and performance.
The Rhetorical Dynamics of Judicial Situations: Joseph Story, Ciceronian Rhetoric, and the Judicial Response to American Slavery
Authors: O'Rourke Sean Patrick
Published: November 2012

This essays offers a rhetorical interpretation of judicial opinions Joseph Story wrote in four U.S. Supreme Court cases concerned with the slavery question: U.S. v. La Jeune Eugenie (1822), Groves v. Slaughter (1841), U.S. v. Amistad (1841), and Prigg v. Pennsylvania (1842). I argue that Story, a jurist trained in the intellectual traditions of the early republic, performed judicial argument as a kind of rhetorical action dependent upon Ciceronian controversia, a mental habit of arguing pro et contra on any matter in dispute. In consequence of this approach to judicial argument, Story's opinions do not represent a choice between positive law or natural law, neither do they represent a commitment to legal instrumentalism or legal formalism; rather they present controversial responses to rhetorical situations broadly conceived.
Invention in James M. Hoppin'sHOMILETICS: Scope and Classicism in Late Nineteenth-Century American Rhetoric
Authors: Whitburn Merrill D.
Published: November 2012

Although conventional views about late nineteenth-century rhetoric highlight a shift from oratory to composition and from classical rhetoric to a “new” rhetoric with origins in Scottish rhetoricians (with a loss of scholarship and quality), James M. Hoppin's Homiletics can be grouped with an increasing number of works that complicate such views. Hoppin focuses on oratory; reveals an especially broad and scholarly knowledge of classical, religious, and foreign rhetorics; uses a complex of ideas called “uniformitarianism” to justify his primary focus on classical rhetoric; and achieves high quality. His concept of invention has both classical and Christian roots in a complex relationship reflecting both scope and narrowness.