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The genome of Rhodobacter sphaeroides encodes the components of two distinct pathways for salvaging cobinamide (Cbi), a precursor of adenosylcobalamin (AdoCbl, coenzyme [B.sub.12]). One pathway, conserved among bacteria, depends on a bifunctional kinase/guanylyltransferase (CobP) enzyme to convert adenosylcobinamide (AdoCbi) to AdoCbi-phosphate (AdoCbi-P), an intermediate in de novo AdoCbl biosynthesis. The other pathway, of archaeal origin, depends on an AdoCbi amidohydrolase (CbiZ) enzyme to generate adenosylcobyric acid (AdoCby), which is converted to AdoCbi-P by the AdoCbi-P synthetase (CobD) enzyme. Here we report that R. sphaeroides strain 2.4.1 synthesizes AdoCbl de novo and that it salvages Cbi using both of the predicted Cbi salvaging pathways. AdoCbl produced by R. sphaeroides was identified and quantified by high-performance liquid chromatography and bioassay. The deletion of cobB (encoding an essential enzyme of the de novo corrin ring biosynthetic pathway) resulted in a strain of R. sphaeroides that would not grow on acetate in the absence of exogenous corrinoids. The results from a nutritional analysis showed that the presence of either CbiZ or CobP was necessary and sufficient for Cbi salvaging, that CbiZ-dependent Cbi salvaging depended on the presence of CobD, and that CobP-dependent Cbi salvaging occurred in a [cbiZ.sup.+] strain. Possible reasons why R. sphaeroides maintains two distinct pathways for Cbi salvaging are discussed.

Bacterial biofilms are a major and ongoing concern for public health, featuring both inherited genetic resistance traits and a conferred innate tolerance to traditional antibiotic therapies. Consequently, there is a growing need for novel methods of drug delivery, to increase the efficacy of antimicrobial agents. This research evaluated the anti-biofilm and bactericidal effects of ultrasound responsive gas-microbubbles (MBs) of either air or nitric oxide, using an in vitro Pseudomonas aeruginosa biofilm model grown in artificial wound medium. The four lipid-based MB formulations evaluated were room-air MBs (RAMBs) and nitric oxide MBs (NOMBs) with no electrical charge, as well as cationic (+) RAMBs+ and NOMBs+. Two principal treatment conditions were used: i) ultrasound stimulated MBs only, and ii) ultrasound stimulated MBs with a sub-inhibitory concentration (4 µg/mL) of the antibiotic gentamicin. The total treatment time was divided into a 60 second passive MB interaction period prior to 40 second ultrasound exposure; each MB formulation was tested in triplicate. Ultrasound stimulated RAMBs and NOMBs without antibiotic achieved reductions in biofilm biomass of 93.3% and 94.0%, respectively. Their bactericidal efficacy however was limited, with a reduction in culturable cells of 26.9% and 65.3%, respectively. NOMBs with sub-inhibitory antibiotic produced the most significant reduction in biofilm biomass, corresponding to a 99.9% (SD ± 5.21%); and a 99.9% (SD ± 0.07%) (3-log) reduction in culturable bacterial cells. Cationic MBs were initially manufactured to promote binding of MBs to negatively charged biofilms, but these formulations also demonstrated intrinsic bactericidal properties. In the absence of antibiotic, the bactericidal efficacy of RAMB+ and NOMB+ was greater that of uncharged counterparts, reducing culturable cells by 84.7% and 86.1% respectively; increasing to 99.8% when combined with antibiotic. This study thus demonstrates the anti-biofilm and bactericidal utility of ultrasound stimulated MBs, and specifically is the first to demonstrate the efficacy of a NOMB for the dispersal and potentiation of antibiotics against bacterial biofilms in vitro. Importantly the biofilm system and complex growth-medium were selected to recapitulate key morphological features of in vivo biofilms. The results us offer new insight for the development of new clinical treatments, for example, in chronic wounds. [ABSTRACT FROM AUTHOR]

Objective: Registration between phases in 4D cardiac MRI is essential for reconstructing high-quality images and appreciating the dynamics. Complex motion and limited image quality make it challenging to design regularization functionals. We propose to introduce a motion representation model (MRM) into a registration network to impose customized, site-specific, and spatially variant prior for cardiac motion. Methods: We propose a novel approach to regularize deep registration with a deformation vextor field (DVF) representation model using computed tomography angiography (CTA). In the form of a convolutional auto-encoder, the MRM was trained to capture the spatially variant pattern of feasible DVF Jacobian. The CTA-derived MRM was then incorporated into an unsupervised network to facilitate MRI registration. In the experiment, 10 CTAs were used to derive the MRM. The method was tested on 10 0.35 T scans in long-axis view with manual segmentation and 15 3 T scans in short-axis view with tagging-based landmarks. Results: Introducing the MRM improved registration accuracy and achieved 2.23, 7.21, and 4.42 mm 80% Hausdorff distance on left ventricle, right ventricle, and pulmonary artery, respectively, and 2.23 mm landmark registration error. The results were comparable to carefully tuned SimpleElastix, but reduced the registration time from 40 s to 0.02 s. The MRM presented good robustness to different DVF sample generation methods. Conclusion: The model enjoys high accuracy as meticulously tuned optimization model and the efficiency of deep networks. Significance: The method enables model to go beyond the quality limitation of MRI. The robustness to training DVF generation scheme makes the method attractive to adapting to the available data and software resources in various clinics. [ABSTRACT FROM AUTHOR]

NarX-NarL and NarQ-NarP are paralogous two-component regulatory systems that control Escherichia coli gene expression in response to the respiratory oxidants nitrate and nitrite. Nitrate stimulates the autophosphorylation rates of the NarX and NarQ sensors, which then phosphorylate the response regulators NarL and NarP to activate and repress target operon transcription. Here, we investigated both the autophosphorylation and dephosphorylation of soluble sensors in which the maltose binding protein (MBP) has replaced the amino-terminal transmembrane sensory domain. The apparent affinities ([K.sub.m]) for ADP were similar for both proteins, about 2 [micro]M, whereas the affinity of MBP-NarQ for ATP was lower, about 23 [micro]M. At a saturating concentration of ATP, the rate constant of MBP-NarX autophosphorylation (about 0.5 x [10.sup.-4] [s.sup.-1]) was lower than that observed for MBP-NarQ (about 2.2 x [10.sup.-4] [s.sup.-1]). At a saturating concentration of ADP, the rate constant of dephosphorylation was higher than that of autophosphorylation, about 0.03 [s.sup.-1] for MBP-NarX and about 0.01 [s.sup.-1] for MBP-NarQ. For other studied sensors, the published affinities for ADP range from about 16 [micro]M (KinA) to about 40 [micro]M (NtrB). This suggests that only a small proportion of NarX and NarQ remain phosphorylated in the absence of nitrate, resulting in efficient response regulator dephosphorylation by the remaining unphosphorylated sensors.

To purchase or authenticate to the full-text of this article, please visit this link: http://dx.doi.org/10.1111/j.1523-1739.2006.00557.x Byline: MICHAEL A. GRAY ([dagger]*), SANDRA L. BALDAUF ([dagger]), PETER J. MAYHEW ([dagger]), JANE K. HILL ([dagger]) Keywords: habitat modification; meta-analysis; phylogeny; tropical diversity Abstract: Abstract: Anthropogenic habitat disturbance is a major threat to tropical forests and understanding the ecological consequences of this disturbance is crucial for the conservation of biodiversity. There have been many attempts to determine the ecological traits associated with bird species' vulnerability to disturbance, but no attempt has been made to synthesize these studies to show consensus. We analyzed data from 57 published studies (covering 1214 bird species) that investigated the response of tropical bird assemblages to moderate forest disturbance (e.g., selective logging). Our results show that the mean abundance of species from six commonly reported feeding guilds responded differently to disturbance and that species' ecological traits (body size, local population size, and geographic range size) and evolutionary relationships may influence responses in some guilds. Granivore abundance increased significantly and insectivore and frugivore abundance decreased significantly following disturbance. These general conclusions were robust to the effects of ecological traits and phylogeny. Responses of carnivores, nectarivores, and omnivores were less clear, but analyses that accounted for phylogeny indicated that these guilds declined following disturbance. In contrast to the other guilds, the reported responses of carnivores and nectarivores differed among regions (Asia vs. Neotropics) and were influenced by the sampling protocols used in different studies (e.g., time since disturbance), which may explain the difficulty in detecting general responses to disturbance in these guilds. Overall, general patterns governed the responses of species to habitat disturbance, and the differential responses of guilds suggested that disturbance affects trophic organization and thus ecosystem functioning. Abstract (Spanish): Respuesta de Gremios Alimentarios de Aves a la Perturbacion de Bosques Tropicales Resumen: La perturbacion antropogenica del habitat es una de las principales amenazas a los bosques tropicales y el entendimiento de las consecuencias de esta perturbacion es crucial para la conservacion de la biodiversidad. Ha habido muchos intentos para determinar las caracteristicas ecologicas asociadas con la vulnerabilidad de especies de aves a la perturbacion, pero no ha habido intentos para sintetizar estos estudios para mostrar consenso. Analizamos datos de 57 estudios publicados (abarcando 1214 especies de aves) que investigaron la respuesta de ensambles de aves tropicales a la perturbacion moderada de bosques (e.g., tala selectiva). Nuestros resultados muestran que la abundancia promedio de especies de seis gremios alimentarios comunmente reportados respondio distintamente a la perturbacion y que las caracteristicas ecologicas (tamano corporal, tamano de la poblacion local y extension del rango geografico) y las relaciones evolutivas de las especies pueden influir en las respuestas de algunos gremios. La abundancia de granivoros incremento significativamente y la abundancia de insectivoros y frugivoros disminuyo significativamente despues de la perturbacion. Estas conclusiones generales fueron robustas para los efectos de las caracteristicas ecologicas y filogenia. Las respuestas de carnivoros, necatarivoros y omnivoros fueron menos claras, pero los analisis que consideraron la filogenia indicaron que estos gremios declinaron despues de la perturbacion. En contraste con otros gremios, las respuestas reportadas para carnivoros y nectarivoros fueron difirieron entre regiones (Asia vs. Neotropico) y fueron influenciadas por los protocolos de muestreo utilizados en diferentes estudios (e.g., tiempo despues de la perturbacion), lo cual puede explicar la dificultad para detectar respuestas generales a la perturbacion en estos gremios. En conjunto, imperaron patrones generales en las respuestas de especies a la perturbacion del habitat, y las respuestas diferenciales de los gremios sugirieron que la perturbacion afecta la organizacion trofica y por lo tanto al funcionamiento del ecosistema. Author Affiliation: ([dagger])Department of Biology (Area 18), University of York, York YO10 5YW, United Kingdom Article History: Paper submitted December 19, 2005; revised manuscript accepted April 18, 2006. Article note: (*) email mg162@york.ac.uk