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.

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.

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.

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.

[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.

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.

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.

Effect of congenital heart defects on language development in toddlers with Down syndrome.

BACKGROUND: Down syndrome (DS, OMIM #190685) is the most commonly identified genetic form of intellectual disability with congenital heart defect (CHD) occurring in 50% of cases. With advances in surgical techniques and an increasing lifespan, this has necessitated a greater understanding of the neurodevelopmental consequences of CHDs. Herein, we explore the impact of CHD on language development in children with DS. METHODS: Twenty-nine children with DS were observed systematically in parent-child interactions using the Communication Play Protocol to evaluate their language use; they also completed the Mullen Scales of Early Learning and MacArthur Communication Development Inventory. Mean ages were 31.2 months for children with DS and CHD (DS + CHD, n = 12) and 32.1 months for children with DS and a structurally normal heart (DS - CHD, n = 17). RESULTS: Compared with the DS - CHD controls, the DS + CHD group revealed lower scores in multiple areas, including fine motor skills and expressive and receptive vocabulary. Whereas most differences were not statistically significant, the Communication Development Inventory word count and symbol-infused joint engagement differed significantly (P < 0.01) and marginally (P = 0.09) between groups. CONCLUSIONS: Finding that CHDs may account for part of the variation in language delay allows us to consider the specific mechanisms underlying the impact of CHDs on language acquisition in children with DS. Conclusions from this first study on early language outcomes of children with DS + CHD may be useful for clinicians in providing developmental surveillance and early intervention programmes with specific emphasis on language therapy as part of long-term follow-up for children with DS + CHD.

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.

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.

Fatal case of Weeksella virosa sepsis.

Weeksella virosa is an aerobic Gram-negative rod that has rarely been reported to cause infection. We describe a fatal case of W. virosa sepsis in a young female with end-stage renal disease, report three additional cases of W. virosa infection, and review the literature regarding this infection.

Largest Lyapunov exponents for lattices of interacting classical spins.

We investigate how generic the onset of chaos in interacting many-body classical systems is in the context of lattices of classical spins with nearest-neighbor anisotropic couplings. Seven large lattices in different spatial dimensions were considered. For each lattice, more than 2000 largest Lyapunov exponents for randomly sampled Hamiltonians were numerically computed. Our results strongly suggest the absence of integrable nearest-neighbor Hamiltonians for the infinite lattices except for the trivial Ising case. In the vicinity of the Ising case, the largest Lyapunov exponents exhibit a power-law growth, while further away they become rather weakly sensitive to the Hamiltonian anisotropy. We also provide an analytical derivation of these results.

Concerted, highly asynchronous, enzyme-catalyzed [4 + 2] cycloaddition in the biosynthesis of spinosyn A; computational evidence.

A theoretical study has been carried out on model systems to study a recently reported, (Nature, 2011, 473, 109) biosynthetic, [4 + 2] cycloaddition catalyzed by a stand-alone enzyme (the cyclase SpnF). It was suggested in this paper that SpnF is the first known example of a Diels-Alderase (DA). In the present study, for a model system of the substrate a transition structure was found with density functional calculations (DFT). In addition, the intrinsic reaction coordinate calculations indicated that the transition structure is that of a concerted, but highly asynchronous, DA reaction. Based on the DFT and Møller-Plesset second order calculations the activation energy was estimated to be about 15 kcal mol(-1). The results of a natural population analysis indicated that there is significant charge transfer in the transition state, and it is proposed that possibly the enzyme plays a dual role of not only folding the substrate into the proper conformation for the DA reaction to occur, but also lowering its activation energy by stabilization of the highly polarized transition structure.

Physical constraints on sesquiterpene diversity arising from cyclization of the eudesm-5-yl carbocation.

The biogenic origins of complex cyclic terpenes derive from the interplay of enzymes and the intrinsic reactivity of carbocation species at major branch-points along intramolecular cyclization pathways to ultimately determine the distribution of terpene skeletal types in nature. Solanaceous plants biosynthesize chemical defense compounds, largely derived from the eremophilane and spirovetivane-type sesquiterpenes. These hydrocarbon skeletons share a common biogenic origin, stemming from alternative Wagner-Meerwein rearrangements of the eudesm-5-yl carbocation during the cyclization of farnesyl pyrophosphate (FPP) catalyzed by sesquiterpene synthases. While the spirojatamane skeleton shares the same carbocation intermediate, this class of sesquiterpenes has not been reported in the Solanaceae and is exceedingly rare in nature. To investigate the physical basis for alternative rearrangements of the eudesm-5-yl carbocation, we carried out quantum mechanics (QM) analyses to calculate the allowable conformations, energies, and transition states linking conformers of the eudesm-5-yl carbocation to the eremophilene, spirovetivane, and spirojatamane skeletons. Additionally, we conducted parallel investigations on simplified decalin carbocation systems to examine the contribution of ring substituents to allowable conformations and rearrangement pathways. Our study reveals that ring substituents expand the conformational space accessible to the eudesm-5-yl carbocation while sterically blocking rearrangements in certain contexts. From our analysis, we define a conformational threshold for each possible rearrangement based on dihedral angles describing transition state geometry. Further, our calculations indicate that methylene migration rearrangements leading to spiro compounds are thermodynamically dominant in the eudesm-5-yl and simpler decalin carabocation systems. Interestingly, the theoretical abundance of sesquiterpene skeletal types arising from the intrinsic reactivity of the eudesm-5-yl carbocation stands in sharp contrast to their currently known natural abundance. The implications of these results for the catalytic tragectories catalyzed by sesquiterpene synthases are discussed.

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.