Draft genome sequences of five recent human uropathogenic Escherichia coli isolates

This study reports the release of draft genome sequences of five isolates of uropathogenic Escherichia coli (UPEC), isolated from patients suffering from uncomplicated cystitis in 2012 in Ann Arbor, Michigan. Phylogenetic analyses revealed that these strains belonged to E. coli phylogroups B2 and D and are closely related to known UPEC strains. Comparative genomic analysis revealed that more conserved proteins were shared between these recent isolates and UPEC strains causing cystitis than those causing pyelonephritis. Additional genomic comparisons identified that three isolates encode a type III secretion system (T3SS) and a putative T3SS effector gene cluster along with an invasin‐like outer membrane protein. The presence of T3SS genes is a rare occurrence among UPEC strains. These genomes further substantiate the heterogeneity of the gene pool of UPEC and provide a foundation for comparative genomic studies using recent clinical isolates.This publication briefly describes the draft genomes of five recent human uropathogenic (UPEC) Escherichia coli isolates. UPEC are of increasing importance to human health. The genomes of these new isolates are clearly and simply described and will be of great utility and interest to this research community.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/136326/1/fim12059.pd

Proteobactin and a yersiniabactin-related siderophore mediate iron acquisition in Proteus mirabilis

Proteus mirabilis causes complicated urinary tract infections (UTIs). While the urinary tract is an iron-limiting environment, iron acquisition remains poorly characterized for this uropathogen. Microarray analysis of P. mirabilis HI4320 cultured under iron limitation identified 45 significantly upregulated genes ( P  ≤  0.05) that represent 21 putative iron-regulated systems. Two gene clusters, PMI0229-0239 and PMI2596-2605, encode putative siderophore systems. PMI0229-0239 encodes a non-ribosomal peptide synthetase-independent siderophore system for producing a novel siderophore, proteobactin. PMI2596-2605 are contained within the high-pathogenicity island, originally described in Yersinia pestis , and encodes proteins with apparent homology and organization to those involved in yersiniabactin production and uptake. Cross-feeding and biochemical analysis shows that P. mirabilis is unable to utilize or produce yersiniabactin, suggesting that this yersiniabactin-related locus is functionally distinct. Only disruption of both systems resulted in an in vitro iron-chelating defect; demonstrating production and iron-chelating activity for both siderophores. These findings clearly show that proteobactin and the yersiniabactin-related siderophore function as iron acquisition systems. Despite the activity of both siderophores, only mutants lacking the yersiniabactin-related siderophore have reduced fitness in vivo . The fitness requirement for the yersiniabactin-related siderophore during UTI shows, for the first time, the importance of siderophore production in vivo for P. mirabilis .Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/79111/1/MMI_7317_sm_FigS1-S2_TabS1-S3.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/79111/2/j.1365-2958.2010.07317.x.pd

Astabiotics: Antimicrobial Signal Transduction Activators

poster abstractThe increasing prevalence of multi-drug resistant Gram-negative bacteria is a major public health concern. All available antibiotics are inhibitors of targets essential for virulence or growth. CpxRA is a highly conserved bacterial signal transduction system that responds to extracytoplasmic membrane stress. CpxA is a sensor with kinase and phosphatase activity; upon activation, CpxA donates a phosphate group to CpxR, activating a transcriptional response. Activation of CpxRA reduces the flow of protein traffic through the cytoplasmic membrane, dramatically reducing the expression of virulence determinants. Activation of CpxRA abolishes the virulence of Salmonella Typhimurium in mice. We found that activation of CpxRA crippled the ability of Haemophilus ducreyi to cause disease in experimentally infected human volunteers. Using an Escherichia coli reporter strain, we developed a high throughput screen to detect compounds that activate CpxRA. In a pilot screen of 36,000 compounds, we identified 1 class of compounds that shifts the equilibrium of CpxA to kinase activity, activating CpxR. Based on its potency, the calculated effective dose of the lead compound (a nitroindole) was 10 mg/kg. Female mice tolerated 100 mg/kg of the nitroindole given twice a day for 3 days. A CpxRA activating mutant constructed in uropathogenic E. coli (UPEC) was severely impaired in a murine urinary tract infection model; thus, activation of CpxRA is a valid treatment strategy for UPEC. However, when female mice were challenged with UPEC and treated with 100 mg/kg of the nitroindole using the schedule above, there were no differences in the recovered CFU in the urine, bladder, and kidney of sham and compound-treated mice. Future studies will include medicinal optimization of the nitroindole and identification and optimization other leads that activate CpxRA. Although our pilot test of efficacy was negative, astabiotics have great potential as broad-spectrum, adjunctive therapies to existing antimicrobials for treatment of Gram-negative infections

Актуальність впровадження систем газового обліку в сучасних умовах

Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized.QC 20150505</p

Effect of the integration method on the accuracy and computational efficiency of free energy calculations using thermodynamic integration

Although calculations of free energy using molecular dynamics simulations have gained significant importance in the chemical and biochemical fields, they still remain quite computationally intensive. Furthermore, when using thermodynamic integration, numerical evaluation of the integral of the Hamiltonian with respect to the coupling parameter may introduce unwanted errors in the free energy. In this paper, we compare the performance of two numerical integration techniques-the trapezoidal and Simpson's rules and propose a new method, based on the analytic integration of physically based fitting functions that are able to accurately describe the behavior of the data. We develop and test our methodology by performing detailed studies on two prototype systems, hydrated methane and hydrated methanol, and treat Lennard-Jones and electrostatic contributions separately. We conclude that the widely used trapezoidal rule may introduce systematic errors in the calculation, but these errors are reduced if Simpson's rule is employed, at least for the electrostatic component. Furthermore, by fitting thermodynamic integration data, we are able to obtain precise free energy estimates using significantly fewer data points (5 intermediate states for the electrostatic component and 11 for the Lennard-Jones term), thus significantly decreasing the associated computational cost. Our method and improved protocol were successfully validated by computing the free energy of more complex systems hydration of 2-methylbutanol and of 4-nitrophenol-thus paving the way for widespread use in solvation free energy calculations of drug molecules

Factors regulating the Great Calcite Belt in the Southern Ocean and its biogeochemical significance

The Great Calcite Belt (GCB) is a region of elevated surface reflectance in the Southern Ocean (SO) covering ~16% of the global ocean and is thought to result from elevated, seasonal concentrations of coccolithophores. Here we describe field observations and experiments from two cruises that crossed the GCB in the Atlantic and Indian sectors of the SO. We confirm the presence of coccolithophores, their coccoliths, and associated optical scattering, located primarily in the region of the subtropical, Agulhas, and Subantarctic frontal regions. Coccolithophore-rich regions were typically associated with high-velocity frontal regions with higher seawater partial pressures of CO2 (pCO2) than the atmosphere, sufficient to reverse the direction of gas exchange to a CO2 source. There was no calcium carbonate (CaCO3) enhancement of particulate organic carbon (POC) export, but there were increased POC transfer efficiencies in high-flux particulate inorganic carbon regions. Contemporaneous observations are synthesized with results of trace-metal incubation experiments, 234Th-based flux estimates, and remotely sensed observations to generate a mandala that summarizes our understanding about the factors that regulate the location of the GCB

The Palomar Testbed Interferometer

The Palomar Testbed Interferometer (PTI) is a long-baseline infrared interferometer located at Palomar Observatory, California. It was built as a testbed for interferometric techniques applicable to the Keck Interferometer. First fringes were obtained in July 1995. PTI implements a dual-star architecture, tracking two stars simultaneously for phase referencing and narrow-angle astrometry. The three fixed 40-cm apertures can be combined pair-wise to provide baselines to 110 m. The interferometer actively tracks the white-light fringe using an array detector at 2.2 um and active delay lines with a range of +/- 38 m. Laser metrology of the delay lines allows for servo control, and laser metrology of the complete optical path enables narrow-angle astrometric measurements. The instrument is highly automated, using a multiprocessing computer system for instrument control and sequencing.Comment: ApJ in Press (Jan 99) Fig 1 available from http://huey.jpl.nasa.gov/~bode/ptiPicture.html, revised duging copy edi

NGF effects on developing forebrain cholinergic neurons are regionally specific

Nerve growth factor (NGF) has been shown to have an effect on neurons in the central nervous system (CNS). A number of observations suggest that NGF acts as a trophic factor for cholinergic neurons of the basal forebrain and the caudate-putamen. We sought to further characterize the CNS actions of NGF by examining its effect on choline acetyltransferase (ChAT) activity in the cell bodies and fibers of developing neurons of the septum and caudate-putamen. ChAT activity was increased after even a single NGF injection. Interestingly, the magnitude of the effect of multiple NGF injections suggested that repeated treatments may augment NGF actions on these neurons. The time-course of the response to NGF was followed after a single injection on postnatal day (PD) 2. NGF treatment produced long-lasting increases in ChAT activity in septum, hippocampus and caudate-putamen. The response in cell body regions (septum, caudate-putamen) was characterized by an initial lag period of approximately 24 hr, a rapid rise to maximum values, a plateau phase and a return to baseline. The response in hippocampus was delayed by 48 hr relative to that in septum, indicating that NGF actions on ChAT were first registered in septal cell bodies. Finally, developmental events were shown to have a regionally specific influence on the response of neurons to NGF. For though the septal response to a single NGF injection was undiminished well into the third postnatal week, little or no response was detected in caudate-putamen at that time. In highlighting the potency and regional specificity of NGF effects, these observations provide additional, support for the hypothesis that NGF is a trophic factor for CNS cholinergic neurons.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45403/1/11064_2004_Article_BF00970927.pd

Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease

Molecular docking is a powerful tool used in drug discovery and structural biology for predicting the structures of ligand–receptor complexes. However, the accuracy of docking calculations can be limited by factors such as the neglect of protein reorganization in the scoring function; as a result, ligand screening can produce a high rate of false positive hits. Although absolute binding free energy methods still have difficulty in accurately rank-ordering binders, we believe that they can be fruitfully employed to distinguish binders from nonbinders and reduce the false positive rate. Here we study a set of ligands that dock favorably to a newly discovered, potentially allosteric site on the flap of HIV-1 protease. Fragment binding to this site stabilizes a closed form of protease, which could be exploited for the design of allosteric inhibitors. Twenty-three top-ranked protein–ligand complexes from AutoDock were subject to the free energy screening using two methods, the recently developed binding energy analysis method (BEDAM) and the standard double decoupling method (DDM). Free energy calculations correctly identified most of the false positives (≥83%) and recovered all the confirmed binders. The results show a gap averaging ≥3.7 kcal/mol, separating the binders and the false positives. We present a formula that decomposes the binding free energy into contributions from the receptor conformational macrostates, which provides insights into the roles of different binding modes. Our binding free energy component analysis further suggests that improving the treatment for the desolvation penalty associated with the unfulfilled polar groups could reduce the rate of false positive hits in docking. The current study demonstrates that the combination of docking with free energy methods can be very useful for more accurate ligand screening against valuable drug targets

Antecedents and Outcomes of Managing Diversity in a UK Context: Test of a Mediation Model

Extant research on diversity management has primarily examined the main effects of diversity management practices on outcomes from an organizational perspective. Meta-analysis in this field corroborates the conclusion that this approach is unable to account for the outcomes of diversity management effectively. The current study extends the literature by examining organizational antecedents of diversity management practices (DMP). This study also examines the mediating influences of perception of overall justice (POJ) and social exchange with organization (SEWO) on the relationships between DMP and work outcomes of career satisfaction and turnover intention. Results of data obtained from a cross section of 191 minority employees in UK revealed: (i) the reasons why organisations adopted and implemented DMP influenced employees’ outcomes of turnover intention and career satisfaction; (ii) the relationship between diversity management and social exchange with organization is mediated by perception of overall justice; (iii) social exchange with organization relates to increased career satisfaction; and (iv) DMP related positively to career satisfaction through perception of overall justice and SEWO