Draft Genome Sequence Determination for Cystic Fibrosis and Chronic Granulomatous Disease Burkholderia multivorans Isolates

Burkholderia multivorans is a Gram-negative bacterium and a member of the Burkholderia cepacia complex, which is frequently associated with respiratory infections in people with cystic fibrosis (CF) and chronic granulomatous disease (CGD). We are reporting the genome sequences of 4 B. multivorans strains, 2 from CF patients and 2 from CGD patients.     

Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling

Soluble epoxide hydrolase (sEH) is an enzyme involved in drug metabolism that catalyzes the hydrolysis of epoxides to form their corresponding diols. sEH has a broad substrate range and shows high regio- and enantioselectivity for nucleophilic ring opening by Asp333. Epoxide hydrolases therefore have potential synthetic applications. We have used combined quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics (MD) simulations (at the AM1/CHARMM22 level) and high-level ab initio (SCS-MP2) QM/MM calculations to analyze the reactions, and determinants of selectivity, for two substrates: trans-stilbene oxide (t-SO) and trans-diphenylpropene oxide (t-DPPO). The calculated free energy barriers from the QM/MM (AM1/CHARMM22) umbrella sampling MD simulations show a lower barrier for phenyl attack in t-DPPO, compared with that for benzylic attack, in agreement with experiment. Activation barriers in agreement with experimental rate constants are obtained only with the highest level of QM theory (SCS-MP2) used. Our results show that the selectivity of the ring-opening reaction is influenced by several factors, including proximity to the nucleophile, electronic stabilization of the transition state, and hydrogen bonding to two active site tyrosine residues. The protonation state of His523 during nucleophilic attack has also been investigated, and our results show that the protonated form is most consistent with experimental findings. The work presented here illustrates how determinants of selectivity can be identified from QM/MM simulations. These insights may also provide useful information for the design of novel catalysts for use in the synthesis of enantiopure compounds.     

Structural studies of the spinosyn rhamnosyltransferase, SpnG

Spinosyns A and D (spinosad), like many other complex polyketides, are tailored near the end of their biosyntheses through the addition of sugars. SpnG, which catalyzes their 9-OH rhamnosylation, is also capable of adding other monosaccharides to the spinosyn aglycone (AGL) from TDP-sugars; however, the substitution of UDP-D-glucose for TDP-D-glucose as the donor substrate is known to result in a >60000-fold reduction in k(cat). Here, we report the structure of SpnG at 1.65 ? resolution, SpnG bound to TDP at 1.86 ? resolution, and SpnG bound to AGL at 1.70 ? resolution. The SpnG-TDP complex reveals how SpnG employs N202 to discriminate between TDP- and UDP-sugars. A conformational change of several residues in the active site is promoted by the binding of TDP. The SpnG-AGL complex shows that the binding of AGL is mediated via hydrophobic interactions and that H13, the potential catalytic base, is within 3 ? of the nucleophilic 9-OH group of AGL. A model for the Michaelis complex was constructed to reveal the features that allow SpnG to transfer diverse sugars; it also revealed that the rhamnosyl moiety is in a skew-boat conformation during the transfer reaction.     

Circulating isoflavonoid levels in CD-1 mice: effect of oral versus subcutaneous delivery and frequency of administration

The CD-1 mouse is a commonly used animal model to understand the biological effects of early-life exposure to soy isoflavones in infants. Most studies using CD-1 mice have administered isoflavones by daily subcutaneous injection, while infants receive oral feeds every few hours. The study objectives were to compare the total serum levels of genistein (GEN), daidzein (DAI) and the DAI metabolites equol and O-desmethyl-angolensin (O-DMA), after subcutaneous injection and oral dosing and to determine if frequency of oral administration results in different circulating levels of isoflavones using the CD-1 mouse model. From postnatal days 1 to 5, pups randomly received corn oil or soy isoflavones (total daily dose, 0.010 mg DAI+0.025 mg GEN) by subcutaneous injection once a day, orally once a day or orally every 4 hours. On postnatal day 5, 1 h posttreatment, mice were killed and serum was collected. Mice treated with soy isoflavones had higher (P<.05) serum GEN (female: 1895–3391 ng/ml and male: 483–578 ng/ml) and DAI (female: 850–1580 ng/ml and male: 248–322 ng/ml) concentrations versus control (5–20 ng/ml) mice, regardless of route or frequency of administration, and were similar among dosing strategies. Total serum concentrations of GEN and DAI were higher (P<.05) among females (GEN: 2714 ± 393 ng/ml and DAI: 1205 ± 164 ng/ml) than males (GEN: 521 ± 439 ng/ml and DAI: 288 ± 184 ng/ml) across treatment groups. Serum equol and O-DMA concentrations were negligible (<3 ng/ml) across groups. In conclusion, different routes of delivery and frequency of administration resulted in similar total serum levels of GEN, DAI¸ equol or O-DMA.     

Equol production changes over time in postmenopausal women

Equol (EQ) is produced by intestinal bacteria from the soy isoflavone daidzein (DE) in 30%-60% of the population and is believed to provide benefits from soy intake. A robust EQ status definition is lacking, and it is uncertain whether EQ is formed consistently within an individual and ceases upon oral antibiotic treatment. In a randomized, double-blind, placebo-controlled soy intervention trial with 350 postmenopausal women, DE and EQ were analyzed by liquid chromatography/tandem mass spectrometry at baseline and every 6 months over 2.5 years in overnight urine, spot urine and plasma. Equol production changes and status (remaining an EQ producer or nonproducer or changing towards an EQ producer or nonproducer) were assessed. Equol status was determined most dependably by overnight urine applying as cutoff a ratio of EQ/DE≥0.018 with a DE threshold ≥2 nmol/mg creatinine: the soy and placebo groups had approximately 30% consistent EQ producers during the study, but 14% and 35%, respectively, changed EQ status (mean 1.4-1.7 times), while 27% and 17%, respectively, had antibiotic treatment (P<.01 for inverse association). No significant trend in change of EQ production or status was observed when overnight urine was limited to collections closest to before and after antibiotic treatment. Similarly, antibiotic type or class, duration, dose or time between antibiotic treatment and overnight urine collection showed no consistent influence on EQ production. Equol production can markedly change intraindividually over 2.5 years, and antibiotic treatment impacts it inconsistently. Factors other than antibiotic treatment must be considered as causes for EQ production changes.     

An acoustic glucose sensor

In vivo glucose monitoring is required for tighter glycaemic control. This report describes a new approach to construct a miniature implantable device based on a magnetic acoustic resonance sensor (MARS). A ≈ 600-800 nm thick glucose-responsive poly(acrylamide-co-3-acrylamidophenylboronic acid) (poly(acrylamide-co-3-APB)) film was polymerised on the quartz disc (12 mm in diameter and 0.25 mm thick) of the MARS. The swelling/shrinking of the polymer film induced by the glucose binding to the phenylboronate caused changes in the resonance amplitude of the quartz disc in the MARS. A linear relationship between the response of the MARS and the glucose concentration in the range ≈ 0-15 mM was observed, with the optimum response of the MARS sensor being obtained when the polymer films contained ≈ 20 mol% 3-APB. The MARS glucose sensor also functioned under flow conditions (9 μl/min) with a response almost identical to the sensor under static or non-flow conditions. The results suggest that the MARS could offer a promising strategy for developing a small subcutaneously implanted continuous glucose monitor.     

Lead optimisation of pyrazoles as novel FPR1 antagonists

Optimisation of a series of pyrazole inhibitors of the human FPR1 receptor has been achieved. The use of an in vitro media loss assay was utilised to identify sub-series with more robust DMPK profiles. These were subsequently improved to generate analogues with attractive overall profiles.     

Glomerella truncata: another Glomerella species with an atypical mating system

In the genus Glomerella all species studied to date do not fit the usual mating system of heterothallic ascomycetes. This study investigated the mating system of G. truncata (anamorph Colletotrichum truncatum), a pathogen responsible for lentil anthracnose. Twenty-two field isolates from the Canadian prairies were crossed in all possible combinations, including selfings. All isolates also were screened for the presence of the MAT1-1 and MAT1-2 idiomorphs by targeting small conserved areas of the MAT genes (the alpha domain and the high mobility group HMG box) with degenerate primers, and a pair of G. truncata-specific HMG primers (CT21HMG) were designed. The results of the classical mating study suggested that G. truncata is heterothallic. Isolates fell into two incompatibility groups, which is consistent with a bipolar mating system but different from what has been described in other Glomerella species. Molecular screening showed that the HMG box used as a marker for the MAT1-2 idiomorph was present in both partners of fertile crosses in G. truncata, unlike in the typical ascomycete system, but as previously described for two other Glomerella species. G. truncata therefore appears to share unusual mating system characteristics with the other Glomerella species studied to date.     

Systems Dynamic Modeling of a Guard Cell Cl? Channel Mutant Uncovers an Emergent Homeostatic Network Regulating Stomatal Transpiration

Stomata account for much of the 70% of global water usage associated with agriculture and have a profound impact on the water and carbon cycles of the world. Stomata have long been modeled mathematically, but until now, no systems analysis of a plant cell has yielded detail sufficient to guide phenotypic and mutational analysis. Here, we demonstrate the predictive power of a systems dynamic model in Arabidopsis (Arabidopsis thaliana) to explain the paradoxical suppression of channels that facilitate K⁺ uptake, slowing stomatal opening, by mutation of the SLAC1 anion channel, which mediates solute loss for closure. The model showed how anion accumulation in the mutant suppressed the H⁺ load on the cytosol and promoted Ca²⁺ influx to elevate cytosolic pH (pH_i) and free cytosolic Ca²⁺ concentration ([Ca2+]_i), in turn regulating the K⁺ channels. We have confirmed these predictions, measuring pH_i and [Ca2+]_i in vivo, and report that experimental manipulation of pH_i and [Ca2+]_i is sufficient to recover K⁺ channel activities and accelerate stomatal opening in the slac1 mutant. Thus, we uncover a previously unrecognized signaling network that ameliorates the effects of the slac1 mutant on transpiration by regulating the K⁺ channels. Additionally, these findings underscore the importance of H⁺-coupled anion transport for pH_i homeostasis.Guard cells surround stomatal pores in the epidermis of plant leaves and regulate pore aperture to balance the demands for CO₂ in photosynthesis with the need to conserve water by the plant. Transpiration through stomata accounts for much of the 70% of global water usage associated with agriculture, and it has a profound impact on the water and carbon cycles of the world (Gedney et al., 2006; Betts et al., 2007). Guard cells open the pore by transport and accumulation of osmotically active solutes, mainly K⁺ and Cl⁻ and the organic anion malate²⁻ (Mal), to drive water uptake and cell expansion. They close the pore by coordinating the release of these solutes through K⁺ and anion channels at the plasma membrane. The past half-century has generated a wealth of knowledge on guard cell transport, signaling, and homeostasis, resolving the properties of the major transport processes and metabolic pathways for osmotic solute uptake and accumulation, and many of the signaling pathways that control them (Blatt, 2000; Schroeder et al., 2001; McAinsh and Pittman, 2009; Hills et al., 2012). Even so, much of stomatal dynamics remains unresolved, especially how the entire network of transporters in guard cells works to modulate solute flux and how this network is integrated with organic acid metabolism (Wang and Blatt, 2011) to achieve a dynamic range of stomatal apertures.This gap in understanding is most evident in a number of often unexpected observations, many of which have led necessarily to ad hoc interpretations. Among these, recent studies highlighted a diurnal variation in the free cytosolic Ca²⁺ concentration ([Ca2+]_i), high in the daytime despite the activation of primary ion-exporting ATPases, and have been interpreted to require complex levels of regulation (Dodd et al., 2007). Other findings wholly defy intuitive explanation. For example, the tpk1 mutant of Arabidopsis (Arabidopsis thaliana) removes a major pathway for K⁺ flux across the tonoplast and suppresses stomatal closure, yet the mutant has no significant effect on cellular K⁺ content (Gobert et al., 2007). Similarly, the Arabidopsis clcc mutant eliminates the H⁺-Cl⁻ antiporter at the tonoplast; it affects Cl⁻ uptake, reduces vacuolar Cl⁻ content, and slows stomatal opening; however, counterintuitively, it also suppresses stomatal closure (Jossier et al., 2010). In work leading to this study, we observed that the slac1 anion channel mutant of Arabidopsis paradoxically profoundly alters the activities of the two predominant K⁺ channels at the guard cell plasma membrane. The SLAC1 anion channel is a major pathway for anion loss from the guard cells during stomatal closure (Negi et al., 2008; Vahisalu et al., 2008), and its mutation leads to incomplete and slowed closure of stomata in response to physiologically relevant signals of dark, high CO₂, and the water-stress hormone abscisic acid. Guard cells of the slac1 mutant accumulate substantially higher levels of Cl⁻, Mal, and also K⁺ when compared with guard cells of wild-type Arabidopsis (Negi et al., 2008). The latter observation is consistent with additional impacts on K⁺ transport; however, a straightforward explanation for these findings has not been not forthcoming.Quantitative systems analysis offers one approach to such problems. Efforts to model stomatal function generally have been driven by a “top-down” approach (Farquhar and Wong, 1984; Eamus and Shanahan, 2002) and have not incorporated detail essential to understanding the molecular and cellular mechanics that drive stomatal movement. Only recently we elaborated a quantitative systems dynamic approach to modeling the stomatal guard cell that incorporates all of the fundamental properties of the transporters at the plasma membrane and tonoplast, the salient features of osmolite metabolism, and the essential cytosolic pH (pH_i) and [Ca2+]_i buffering characteristics that have been described in the literature (Hills et al., 2012). The model resolved with this approach (Chen et al., 2012b) successfully recapitulated a wide range of known stomatal behaviors, including transport and aperture dependencies on extracellular pH, KCl, and CaCl₂ concentrations, diurnal changes in [Ca2+]_i (Dodd et al., 2007), and oscillations in membrane voltage and [Ca2+]_i thought to facilitate stomatal closure (Blatt, 2000; McAinsh and Pittman, 2009; Chen et al., 2012b). We have used this approach to resolve the mechanism behind the counterintuitive alterations in K⁺ channel activity uncovered in the slac1 mutant of Arabidopsis. Here, we show how anion accumulation in the mutant affects the H⁺ and Ca²⁺ loads on the cytosol, elevating pH_i and [Ca2+]_i, and in turn regulating the K⁺ channels. We have validated the key predictions of the model and, in so doing, have uncovered a previously unrecognized homeostatic network that ameliorates the effects of the slac1 mutant on transpiration from the plant.