Discovering a uniform functional trade-off of the CBC-type 2,3-oxidosqualene cyclases and deciphering its chemical logic.

Many functionally promiscuous plant 2,3-oxidosqualene cyclases (OSCs) have been found, but complete functional reshaping is rarely reported. In this study, we have identified two new plant OSCs: a unique protostadienol synthase (AoPDS) and a common cycloartenol synthase (AoCAS) from Alisma orientale (Sam.) Juzep. Multiscale simulations and mutagenesis experiments revealed that threonine-727 is an essential residue responsible for protosta-13 (17),24-dienol biosynthesis in AoPDS and that the F726T mutant completely reshapes the native function of AoCAS into a PDS function to yield almost exclusively protosta-13 (17),24-dienol. Unexpectedly, various native functions were uniformly reshaped into a PDS function by introducing the phenylalanine → threonine substitution at this conserved position in other plant and non-plant chair-boat-chair-type OSCs. Further computational modeling elaborated the trade-off mechanisms of the phenylalanine → threonine substitution that leads to the PDS activity. This study demonstrates a general strategy for functional reshaping by using a plastic residue based on the decipherment of the catalytic mechanism.

Effects of sodium bicarbonate infusion on mortality in medical–surgical ICU patients with metabolic acidosis—A single-center propensity score matched analysis / Efectos de la infusión de bicarbonato de sodio sobre la mortalidad en pacientes de UCI médico-quirúrgica con acidosis metabólica: un análisis de puntuación de propensión en un solo Centro

Objective Metabolic acidosis is associated with high mortality. Despite theoretical benefits of sodium-bicarbonate (SB), current evidence remains controversial. We investigated SB-related effects on outcomes in ICU patients with metabolic acidosis. Design Retrospective analysis. Setting Academic medical center. Patients or participants 971 ICU patients with metabolic acidosis defined as arterial pH<7.3 and CO2<45mmHg treated between 2012 and 2016. A propensity score (PS) was estimated using logistic regression. Patients were matched in pairs using the PS. Interventions 441 patients were treated with SB 8.4% (SB-group) and n=530 patients were not (control group). Main variables of interest Primary outcome was all-cause mortality at ICU-discharge. Average Treatment Effect (ATE), Average Treatment effect in Treated (ATT), and estimated relative survival effects at 20 days were computed. Results In the full cohort, we observed considerable differences in pH, base excess, additional acidosis-related indices, and ICU mortality (controls 31% vs. SB-group 56%, p<.001) at baseline between the two groups. After PS-matching (n=174 in each group), no significant difference in ICU mortality was observed (controls 32% vs. SB-group 41%; p=.07). Odds ratios (OR) for ATE and ATT showed no association with ICU mortality (OR ATE: 1.08, 95%-CI 0.99–1.17; p=.08; OR ATT 1.09; 95%-CI 0.99–1.2; p=.09). Hazard ratios at 20-days (multivariable HR, matched sample n=348: 1.16, 95%-CI 0.86–1.56, p=.33) showed similar survival in the two study groups. Conclusions We did not observe effects of SB infusion on all-cause mortality in critically ill patients with metabolic acidosis (AU)

Objetivo La acidosis metabólica se asocia con una alta mortalidad. A pesar de los beneficios teóricos del bicarbonato de sodio (BS), la evidencia actual sigue siendo controvertida. Investigamos los efectos relacionados con el BS sobre los resultados en pacientes de la UCI con acidosis metabólica. Diseño Análisis retrospectivo. Ÿmbito Centro médico académico. Pacientes o participante Se incluyeron 971 pacientes de la Unidad de Cuidados Intensivos (UCI) con acidosis metabólica (pH < 7,3, CO2 < 45 mmHg) tratados entre 2012 y 2016. Se calculó una puntuación de propensión (PS) mediante regresión logística. Los pacientes se emparejaron utilizando el PS. Variables de interés principales Intervenciones; 441 pacientes fueron tratados con BS 8,4% (grupo BS) y n = 530 pacientes no (grupo control). Resultados El resultado primario fue la mortalidad por todas las causas al alta de la UCI. Se calcularon el efecto promedio del tratamiento (ATE), el efecto promedio del tratamiento en los tratados (ATT) y los efectos de supervivencia relativa estimados a los 20 días. En la cohorte completa se observaron diferencias considerables en el pH, el exceso de bases y la mortalidad en la UCI (control 31% vs. grupo BS 56%, p < 0,001) al inicio del estudio entre los grupos. Después del emparejamiento de PS (n = 174 en cada grupo), no se observaron diferencias significativas en la mortalidad en la UCI (control 32% vs. grupo BS 41%; p = 0,07). Los odds ratios (OR) para ATE y ATT no mostraron asociación con la mortalidad en la UCI (OR ATE: 1,08, IC 95%; 0,99-1,17; p = 0,08; OR ATT 1,09; IC 95%; 0,99-1,2; p = 0,09). Los cocientes de riesgo a los 20 días (HR multivariable, muestra emparejada n = 348: 1,16, IC 95%; 0,86-1,56, p = 0,33) mostraron una supervivencia comparable. Conclusiones No observamos efectos de la infusión de BS sobre la mortalidad por todas las causas en pacientes con acidosis metabólica (AU)

Computational studies on the sterol-like cyclization of a monodomain class II terpene cyclase.

Recently the first example of a class II terpene cyclase comprised of only a single domain was reported. Class II synthases are a diverse group of enzymes that catalyze exceptionally complex reactions, including the remarkable cyclization of steroids. This discovery of a single-domain enzyme being able to catalyze a steroid-like product contradicted the long-held tenet that complex class II cyclizations required double-domain enzymes. The proposed mechanism for the sterol-like cyclization of a monodomain class II terpene cyclase was studied computationally by using density functional theory (DFT). The complete pathway for the conversion of 5-geranyl-3,4-dihydroxybenzoate to the steroid-like pentacyclic product merosterolic acid A was elucidated. The formation of a tricyclic carbocation intermediate with three cyclohexane rings was found to be a concerted, but asynchronous, cyclization. The formation of the fourth ring proceeds with a low energy activation Friedel-Crafts reaction. Subsequent deprotonation of this pentacyclic system gave as the final product merosterolic acid. The overall conversion was found to be highly exothermic due to the conversion of three C-C double bonds to C-C single bonds.

The accelerated weight histogram method for alchemical free energy calculations.

The accelerated weight histogram method is an enhanced sampling technique used to explore free energy landscapes by applying an adaptive bias. The method is general and easy to extend. Herein, we show how it can be used to efficiently sample alchemical transformations, commonly used for, e.g., solvation and binding free energy calculations. We present calculations and convergence of the hydration free energy of testosterone, representing drug-like molecules. We also include methane and ethanol to validate the results. The protocol is easy to use, does not require a careful choice of parameters, and scales well to accessible resources, and the results converge at least as quickly as when using conventional methods. One benefit of the method is that it can easily be combined with other reaction coordinates, such as intermolecular distances.

Effects of sodium bicarbonate infusion on mortality in medical-surgical ICU patients with metabolic acidosis-A single-center propensity score matched analysis.

OBJECTIVE: Metabolic acidosis is associated with high mortality. Despite theoretical benefits of sodium-bicarbonate (SB), current evidence remains controversial. We investigated SB-related effects on outcomes in ICU patients with metabolic acidosis. DESIGN: Retrospective analysis. SETTING: Academic medical center. PATIENTS OR PARTICIPANTS: 971 ICU patients with metabolic acidosis defined as arterial pH<7.3 and CO2<45mmHg treated between 2012 and 2016. A propensity score (PS) was estimated using logistic regression. Patients were matched in pairs using the PS. INTERVENTIONS: 441 patients were treated with SB 8.4% (SB-group) and n=530 patients were not (control group). MAIN VARIABLES OF INTEREST: Primary outcome was all-cause mortality at ICU-discharge. Average Treatment Effect (ATE), Average Treatment effect in Treated (ATT), and estimated relative survival effects at 20 days were computed. RESULTS: In the full cohort, we observed considerable differences in pH, base excess, additional acidosis-related indices, and ICU mortality (controls 31% vs. SB-group 56%, p<.001) at baseline between the two groups. After PS-matching (n=174 in each group), no significant difference in ICU mortality was observed (controls 32% vs. SB-group 41%; p=.07). Odds ratios (OR) for ATE and ATT showed no association with ICU mortality (OR ATE: 1.08, 95%-CI 0.99-1.17; p=.08; OR ATT 1.09; 95%-CI 0.99-1.2; p=.09). Hazard ratios at 20-days (multivariable HR, matched sample n=348: 1.16, 95%-CI 0.86-1.56, p=.33) showed similar survival in the two study groups. CONCLUSIONS: We did not observe effects of SB infusion on all-cause mortality in critically ill patients with metabolic acidosis.

Regularizing the fast multipole method for use in molecular simulation.

The parallel scaling of classical molecular dynamics simulations is limited by the communication of the 3D fast Fourier transform of the particle-mesh electrostatics methods, which are used by most molecular simulation packages. The Fast Multipole Method (FMM) has much lower communication requirements and would, therefore, be a promising alternative to mesh based approaches. However, the abrupt switch from direct particle-particle interactions to approximate multipole interactions causes a violation of energy conservation, which is required in molecular dynamics. To counteract this effect, higher accuracy must be requested from the FMM, leading to a substantially increased computational cost. Here, we present a regularization of the FMM that provides analytical energy conservation. This allows the use of a precision comparable to that used with particle-mesh methods, which significantly increases the efficiency. With an application to a 2D system of dipolar molecules representative of water, we show that the regularization not only provides energy conservation but also significantly improves the accuracy. The latter is possible due to the local charge neutrality in molecular systems. Additionally, we show that the regularization reduces the multipole coefficients for a 3D water model even more than in our 2D example.

Comparison of false-negative rates and limits of detection following macrofoam-swab sampling of Bacillus anthracis surrogates via Rapid Viability PCR and plate culture.

AIMS: We evaluated the effects of Bacillus anthracis surrogates, low surface concentrations, surface materials and assay methods on false-negative rate (FNR) and limit of detection (LOD95 ) for recovering Bacillus spores using a macrofoam-swab sampling procedure. METHODS AND RESULTS: Bacillus anthracis Sterne or Bacillus atrophaeus Nakamura spores were deposited over a range of low target concentrations (2-500 per coupon) onto glass, stainless steel, vinyl tile and plastic. Samples were assayed using a modified Rapid Viability-PCR (mRV-PCR) method and the traditional plate culture method to obtain FNR and LOD95 results. CONCLUSIONS: Mean FNRs tended to be lower for mRV-PCR compared to culturing, and increased as spore concentration decreased for all surface materials. Surface material, but not B. anthracis surrogate, influenced FNRs with the mRV-PCR method. The mRV-PCR LOD95 was lowest for glass and highest for vinyl tile. LOD95 values overall were lower for mRV-PCR than for the culture method. SIGNIFICANCE AND IMPACT OF STUDY: This study adds to the limited data on FNR and LOD95 for mRV-PCR and culturing methods with low concentrations of B. anthracis sampled from various surface materials by the CDC macrofoam-swab method. These are key inputs for planning characterization and clearance studies for low contamination levels of B. anthracis.

Proteomic signatures differentiating Bacillus anthracis Sterne sporulation on soil relative to laboratory media.

The process of sporulation is vital for the stability and infectious cycle of Bacillus anthracis. The spore is the infectious form of the organism and therefore relevant to biodefense. While the morphological and molecular events occurring during sporulation have been well studied, the influence of growth medium and temperature on the proteins expressed in sporulated cultures is not well understood. Understanding the features of B. anthracis sporulation specific to natural vs. laboratory production will address an important question in microbial forensics. In an effort to bridge this knowledge gap, a system for sporulation on two types of agar-immobilized soils was used for comparison to cultures sporulated on two common types of solid laboratory media, and one liquid sporulation medium. The total number of proteins identified as well as their identity differed between samples generated in each medium and growth temperature, demonstrating that sporulation environment significantly impacts the protein content of the spore. In addition, a subset of proteins common in all of the soil-cultivated samples was distinct from the expression profiles in laboratory medium (and vice versa). These differences included proteins involved in thiamine and phosphate metabolism in the sporulated cultures produced on soils with a notable increase in expression of ATP binding cassette (ABC) transporters annotated to be for phosphate and antimicrobial peptides. A distinct set of ABC transporters for amino acids, sugars and oligopeptides were found in cultures produced on laboratory media as well as increases in carbon and amino acid metabolism-related proteins. These protein expression changes indicate that the sporulation environment impacts the protein profiles in specific ways that are reflected in the metabolic and membrane transporter proteins present in sporulated cultures.

Computational studies on the cyclization of squalene to the steroids and hopenes.

A review of computational studies of the related biosyntheses of steroids and hopenes reported during the last two decades is presented. Computations in the gas phase and those that include the enzyme are covered. Based on the numerical results conclusions have been drawn about the biosynthetic mechansims of these all important biological reactions.

Minimizing the Negative Flavor Attributes and Evaluating Consumer Acceptance of Chocolate Fortified with Peanut Skin Extracts.

In recent years, there has been increased interest in antioxidant-rich products by consumers wanting to enhance the health benefits of their diet. Chocolate has been identified as a natural source of antioxidant compounds, which resulted in the development of polyphenol-enriched chocolate products that are now available commercially. This study investigated the use of phenolic compounds extracted from peanut skins as a novel antioxidant source for the enrichment of milk chocolate. The extracts were encapsulated with maltodextrin to lessen their bitterness. Antioxidant potential of the encapsulated peanut skin extracts was evaluated by the 2,2-diphenyl-1-picrylhydrazl radical quenching assay. Encapsulated peanut skins were found to have a corrected Trolox equivalency of 31.1 µmol/g of chocolate up to 0.8% (w/w). To produce a product with an antioxidant content similar to that of dark chocolate yet which maintained the milder flavor of milk chocolate, the best estimate threshold of encapsulated peanut skin extract in chocolate was 0.9 % (w/w) based on the standard method (American Society of Testing Materials; ASTM E-679). Consumer liking of milk chocolate enhanced by adding subthreshold (0.8 % (w/w)) inclusion levels of encapsulated peanut skin extract was found to be at parity with milk chocolate as a control.

Bacillus anthracis spores germinate extracellularly at air-liquid interface in an in vitro lung model under serum-free conditions.

AIMS: To better understand the parameters that govern spore dissemination after lung exposure using in vitro cell systems. METHODS AND RESULTS: We evaluated the kinetics of uptake, germination and proliferation of Bacillus anthracis Sterne spores in association with human primary lung epithelial cells, Calu-3 and A549 cell lines. We also analysed the influence of various cell culture medium formulations related to spore germination. CONCLUSIONS: We found negligible spore uptake by epithelial cells, but germination and proliferation of spores in the serum-free extracellular environment was evident. Spore germination was appreciably higher in immortalized cell cultures than in primary epithelial cells. Additionally, spores still germinated apically at a mucus-secreting air-liquid interface lung barrier that was devoid of cell culture medium much earlier than medium-only controls. SIGNIFICANCE AND IMPACT OF THE STUDY: The role of lung epithelial cells in B. anthracis spore dissemination after inhalation remains poorly defined and rather controversial. These results are novel as they show spore germination is appreciably enhanced in the presence of lung cells in vitro, however, the cell line and cell state (air-liquid interface vs submerged in medium) dictates the extent of germination and in some cases proliferation.

Biosynthetic Mechanism of Lanosterol: Cyclization.

The remarkable cyclization mechanism of the formation of the 6-6-6-5 tetracyclic lanosterol (a key triterpenoid intermediate in the biosynthesis of cholesterol) from the acyclic 2,3-oxidosqualene catalyzed by oxidosqualene cyclase (OSC) has stimulated the interest of chemists and biologists for over a half century. Herein, the elaborate, state-of-the-art two-dimensional (2D) QM/MM MD simulations have clearly shown that the cyclization of the A-C rings involves a nearly concerted, but highly asynchronous cyclization, to yield a stable intermediate with "6-6-5" rings followed by the ring expansion of the C-ring concomitant with the formation of the D-ring to yield the "6-6-6-5" protosterol cation. The calculated reaction barrier of the rate-limiting step (≈22 kcal mol(-1)) is comparable to the experimental kinetic results. Furthermore all previous experimental mutagenic evidence is highly consistent with the identified reaction mechanism.

Disseminated adenovirus disease in heart transplant recipient presenting with conjunctivitis.

We report a 65-year-old heart transplant recipient who presented with conjunctivitis, likely acquired from a family member who worked at a daycare center during an outbreak of conjunctivitis. He developed a severe adenoviral pneumonitis, which was successfully treated with intravenous cidofovir combined with a reduction of immunosuppression.

Chaotic properties of spin lattices near second-order phase transitions.

We perform a numerical investigation of the Lyapunov spectra of chaotic dynamics in lattices of classical spins in the vicinity of second-order ferromagnetic and antiferromagnetic phase transitions. On the basis of this investigation, we identify a characteristic of the shape of the Lyapunov spectra, the "G-index," which exhibits a sharp peak as a function of temperature at the phase transition, provided the order parameter is capable of sufficiently strong dynamic fluctuations. As part of this work, we also propose a general numerical algorithm for determining the temperature in many-particle systems, where kinetic energy is not defined.

[Ultrasound-guided infraclavicular venipuncture at the junction of the axillary and subclavian veins]. / Ultraschallgestützte infraklavikuläre Punktion am Übergang der V. axillaris in die V. subclavia.

BACKGROUND: Compared to other access routes a central venous catheter inserted via the subclavian vein (VS) is advantageous in terms of patient comfort, care of the puncture site and the infection rate. Puncture of the VS admittedly has a higher risk of mechanical complications but ultrasound guidance can reduce this risk; however, it is technically demanding due to anatomical peculiarities and this access route is therefore used comparatively less frequently. AIM: The aim of the study was to clarify to what extent a modified puncture technique guided by sonography can reduce the risk potential. MATERIAL UND METHODS: A technique is presented in which the infraclavicular insertion site is laterally shifted in the direction of the axillary vein (VA). RESULTS: When the vein is visualized by sonography in the long axis the accompanying artery and the pleura remain outside the ultrasound plane. By doing so, a needle that is strictly guided in the imaging plane can barely damage these structures even if accidentally inserted too deep as they lie outside of the needle trajectory. CONCLUSION: This presented technique can provide benefits for operators experienced in in-plane puncture.

Accelerated weight histogram method for exploring free energy landscapes.

Calculating free energies is an important and notoriously difficult task for molecular simulations. The rapid increase in computational power has made it possible to probe increasingly complex systems, yet extracting accurate free energies from these simulations remains a major challenge. Fully exploring the free energy landscape of, say, a biological macromolecule typically requires sampling large conformational changes and slow transitions. Often, the only feasible way to study such a system is to simulate it using an enhanced sampling method. The accelerated weight histogram (AWH) method is a new, efficient extended ensemble sampling technique which adaptively biases the simulation to promote exploration of the free energy landscape. The AWH method uses a probability weight histogram which allows for efficient free energy updates and results in an easy discretization procedure. A major advantage of the method is its general formulation, making it a powerful platform for developing further extensions and analyzing its relation to already existing methods. Here, we demonstrate its efficiency and general applicability by calculating the potential of mean force along a reaction coordinate for both a single dimension and multiple dimensions. We make use of a non-uniform, free energy dependent target distribution in reaction coordinate space so that computational efforts are not wasted on physically irrelevant regions. We present numerical results for molecular dynamics simulations of lithium acetate in solution and chignolin, a 10-residue long peptide that folds into a ß-hairpin. We further present practical guidelines for setting up and running an AWH simulation.

Small intestinal growth measures are correlated with feed efficiency in market weight cattle, despite minimal effects of maternal nutrition during early to midgestation.

We hypothesized that gestational nutrition would affect calf feed efficiency and small intestinal biology, which would be correlated with feed efficiency. Multiparous beef cows (n = 36) were individually fed 1 of 3 diets from d 45 to 185 of gestation: native grass hay and supplement to meet NRC recommendations (control [CON]), 70% of CON NEm (nutrient restricted [NR]), or a NR diet with a RUP supplement (NR+RUP) to provide similar essential AA as CON. After d 185 of gestation, cows were managed as a single group, and calf individual feed intake was measured with the GrowSafe System during finishing. At slaughter, the small intestine was dissected and sampled. Data were analyzed with calf sex as a block. There was no effect (P ≥ 0.33) of maternal treatment on residual feed intake, G:F, DMI, ADG, or final BW. Small intestinal mass did not differ (P ≥ 0.38) among treatments, although calf small intestinal length tended (P = 0.07) to be greater for NR than NR+RUP. There were no differences (P ≥ 0.20) in calf small intestinal density or jejunal cellularity, proliferation, or vascularity among treatments. Jejunal soluble guanylate cyclase mRNA was greater (P < 0.03) for NR+RUP than CON and NR. Residual feed intake was positively correlated (P ≤ 0.09) with small intestinal mass and relative mass and jejunal RNA content but was negatively correlated (P ≤ 0.09) with jejunal mucosal density and DNA concentration. Gain:feed was positively correlated (P ≤ 0.09) with jejunal mucosal density, DNA, protein, and total cells and was negatively correlated (P ≤ 0.05) with small intestinal relative mass, jejunal RNA, and RNA:DNA. Dry matter intake was positively correlated (P ≤ 0.09) with small intestinal mass, relative mass, length, and density as well as jejunal DNA and protein content, total cells, total vascularity, and kinase insert domain receptor and endothelial nitric oxide synthase 3 mRNA and was negatively correlated (P = 0.02) with relative small intestinal length. In this study, calf performance and efficiency during finishing as well as most measures of small intestinal growth were not affected by maternal nutrient restriction during early and midgestation. Results indicate that offspring small intestinal gene expression may be affected by gestational nutrition even when apparent tissue growth is unchanged. Furthermore, small intestinal size and growth may explain some variation in efficiency of nutrient utilization in feedlot cattle.

The concerted nature of the cyclization of squalene oxide to the protosterol cation.

Concerted A-C ring formation: A concerted, but highly asynchronous, pathway was identified for the formation of rings A-C in the biosynthetic conversion of squalene oxide to the prosterol cation, with ring B being formed in the required boat conformation.

An approximate model for cancellous bone screw fixation.

This paper presents a finite element (FE) model to identify parameters that affect the performance of an improved cancellous bone screw fixation technique, and hence potentially improve fracture treatment. In cancellous bone of low apparent density, it can be difficult to achieve adequate screw fixation and hence provide stable fracture fixation that enables bone healing. Data from predictive FE models indicate that cements can have a significant potential to improve screw holding power in cancellous bone. These FE models are used to demonstrate the key parameters that determine pull-out strength in a variety of screw, bone and cement set-ups, and to compare the effectiveness of different configurations. The paper concludes that significant advantages, up to an order of magnitude, in screw pull-out strength in cancellous bone might be gained by the appropriate use of a currently approved calcium phosphate cement.