Moderate blood alcohol and brain neurovulnerability: Selective depletion of calcium-independent phospholipase A2, omega-3 docosahexaenoic acid, and its synaptamide derivative as a potential harbinger of deficits in anti-inflammatory reserve.

BACKGROUND: Repetitive, highly elevated blood alcohol (ethanol) concentrations (BACs) of 350 to 450 mg/dl over several days cause brain neurodegeneration and coincident neuroinflammation in adult rats localized in the hippocampus (HC), temporal cortex (especially the entorhinal cortex; ECX), and olfactory bulb (OB). The profuse neuroinflammation involves microgliosis, increased proinflammatory cytokines, and elevations of Ca+2 -dependent phospholipase A2 (cPLA2) and secretory PLA2 (sPLA2), which both mobilize proinflammatory ω-6 arachidonic acid (ARA). In contrast, Ca+2 -independent PLA2 (iPLA2) and anti-inflammatory ω-3 docosahexaenoic acid (DHA), a polyunsaturated fatty acid regulated primarily by iPLA2, are diminished. Furthermore, supplemented DHA exerts neuroprotection. Given uncertainties about the possible effects of lower circulating BACs that are common occurring during short- term binges, we examined how moderate BACs affected the above inflammatory events, and the impact of supplemented DHA. METHODS AND RESULTS: Young adult male rats sustaining upper-moderate BACs (~150 mg/dl) from once-daily alcohol intubations were sacrificed with appropriate controls after 1 week. The HC, ECX and OB were quantitatively examined using immunoblotting, neurodegeneration staining, and lipidomics assays. Whereas neurodegeneration, increases in cPLA2 IVA, sPLA2 IIA, and ARA, and microglial activation were not detected, the HC and ECX regions demonstrated significantly reduced iPLA2 levels. Levels of DHA and synaptamide, its anti-inflammatory N-docosahexaenoylethanolamide derivative, also were lower in HC, and DHA supplementation prevented the iPLA2 decrements in HC. Additionally, adult mice maintaining upper-moderate BACs from limited alcohol binges had reduced midbrain iPLA2 levels. CONCLUSIONS: The apparently selective depletion by moderate BACs of the metabolically linked anti-inflammatory triad of hippocampal iPLA2, DHA, and synaptamide, and of iPLA2 in the ECX, potentially indicates an unappreciated deficit in brain anti-inflammatory reserve that may be a harbinger of regional neurovulnerability.

Accelerating the Calculation of Solute-Solvent Interaction Energies through Systematic Molecular Fragmentation.

The method of systematic molecular fragmentation by annihilation (SMFA) is modified to apply to the interaction energy between a solute and solvent, where the solute is a pair of reacting molecules. For NH3 + CH3Cl as the solute, it is shown that SMFA can estimate (to chemical accuracy) the average binding energy of the solute in large water clusters containing up to 160 water molecules, at an appropriate level of electronic structure theory. The SMFA calculation can be carried out in a computation time that makes it feasible to estimate the solvation contribution to free energies of activation and reaction by ensemble averaging.

PARP inhibition in vivo blocks alcohol-induced brain neurodegeneration and neuroinflammatory cytosolic phospholipase A2 elevations.

Chronic alcoholism promotes brain damage that impairs memory and cognition. High binge alcohol levels in adult rats also cause substantial neurodamage to memory-linked regions, notably, the hippocampus (HC) and entorhinal cortex (ECX). Concurrent with neurodegeneration, alcohol elevates poly (ADP-ribose) polymerase-1 (PARP-1) and cytosolic phospholipase A2 (cPLA2) levels. PARP-1 triggers necrosis when excessively activated, while cPLA2 liberates neuroinflammatory ω-6 arachidonic acid. Inhibitors of PARP exert in vitro neuroprotection while suppressing cPLA2 elevations in alcohol-treated HC-ECX slice cultures. Here, we examined in vivo neuroprotection and cPLA2 suppression by the PARP inhibitor, veliparib, in a recognized adult rat model of alcohol-binging. Adult male rats received Vanilla Ensure containing alcohol (ethanol, 7.1 ±â€¯0.3 g/kg/day), or control (dextrose) ±â€¯veliparib (25 mg/kg/day), by gavage 3x daily for 4 days. Rats were sacrificed on the morning after the final binge. HC and ECX neurodegeneration was assessed in fixed sections by Fluoro-Jade B (FJB) staining. Dorsal HC, ventral HC, and ECX cPLA2 levels were quantified by immunoblotting. Like other studies using this model, alcohol binges elevated FJB staining in the HC (dentate gyrus) and ECX, indicating neurodegeneration. Veliparib co-treatment significantly reduced dentate gyrus and ECX neurodegeneration by 79% and 66%, respectively. Alcohol binges increased cPLA2 in the ventral HC by 34% and ECX by 72%, which veliparib co-treatment largely prevented. Dorsal HC cPLA2 levels remained unaffected by alcohol binges, consistent with negligible FJB staining in this brain region. These in vivo results support an emerging key role for PARP in binge alcohol-induced neurodegeneration and cPLA2-related neuroinflammation.

Application of the Systematic Molecular Fragmentation by Annihilation Method to ab Initio NMR Chemical Shift Calculations.

NMR is a powerful tool for obtaining information on the structural characterization and dynamics of proteins, and nucleic acids, and their complexes. The complexity of the spectra is such that elucidation through computational simulation is a much desired thing. However, the size of most structures of interest is such that they remain out of reach of accurate quantum chemical techniques. Fragmentation methods have been shown to be a viable means of reducing the cost of ab initio calculations to enable the prediction of molecular properties of large systems to chemical accuracy. We look at the systematic molecular fragmentation by annihilation method for a model peptide system and show that this procedure reproduces the shielding constants of a full calculation at only a fraction of the cost. Discussion of the considerations needed in applying this method is discussed and comparison made with the results of the similar fragment molecular orbital and ONIOM methods.

PARP Inhibition Prevents Ethanol-Induced Neuroinflammatory Signaling and Neurodegeneration in Rat Adult-Age Brain Slice Cultures.

Using rat adult-age hippocampal-entorhinal cortical (HEC) slice cultures, we examined the role of poly [ADP-ribose] polymerase (PARP) in binge ethanol's brain inflammatory and neurodegenerative mechanisms. Activated by DNA strand breaks, PARP (principally PARP1 in the brain) promotes DNA repair via poly [ADP-ribose] (PAR) products, but PARP overactivation triggers regulated neuronal necrosis (e.g., parthanatos). Previously, we found that brain PARP1 levels were upregulated by neurotoxic ethanol binges in adult rats and HEC slices, and PARP inhibitor PJ34 abrogated slice neurodegeneration. Binged HEC slices also exhibited increased Ca+2-dependent phospholipase A2 (PLA2) isoenzymes (cPLA2 IVA and sPLA2 IIA) that mobilize proinflammatory ω6 arachidonic acid (ARA). We now find in 4-day-binged HEC slice cultures (100 mM ethanol) that PARP1 elevations after two overnight binges precede PAR, cPLA2, and sPLA2 enhancements by 1 day and high-mobility group box-1 (HMGB1), an ethanol-responsive alarmin that augments proinflammatory cytokines via toll-like receptor-4 (TLR4), by 2 days. After verifying that PJ34 effectively blocks PARP activity (↑PAR), we demonstrated that, like PJ34, three other PARP inhibitors-olaparib, veliparib, and 4-aminobenzamide-provided neuroprotection from ethanol. Importantly, PJ34 and olaparib also prevented ethanol's amplification of the PLA2 isoenzymes, and two PLA2 inhibitors were neuroprotective-thus coupling PARP to PLA2, with PLA2 activity promoting neurodegeneration. Also, PJ34 and olaparib blocked ethanol-induced HMGB1 elevations, linking brain PARP induction to TLR4 activation. The results provide evidence in adult brains that induction of PARP1 may mediate dual neuroinflammatory pathways (PLA2→phospholipid→ARA and HMGB1→TLR4→proinflammatory cytokines) that are complicit in binge ethanol-induced neurodegeneration.

Microsolvation within the Systematic Molecular Fragmentation by Annihilation Approach.

We have applied the systematic molecular fragmentation by annihilation (SMFA) fragmentation technique to glycine and DNA base pairs in water clusters, systems for which explicit solvation is believed to be important. The SMFA method was found to be capable of describing the structures, especially in handling the complexity of hydrogen bonding, with energies produced being comparable with those from full molecule results. Thus, the ability to break down large calculations into a manageable time without loss of accuracy shows promise for application to real biological systems for which these effects are relevant.

Can Systematic Molecular Fragmentation Be Applied to Direct Ab Initio Molecular Dynamics?

This paper demonstrates that systematic molecular fragmentation can be applied to direct ab initio molecular dynamics of solvated molecules under periodic boundary conditions. A method for rapidly updating the fragmentation of water at each time step in a simulation is presented and tested. This approach reduces the time required for implementation of systematic molecular fragmentation at each time step, in a highly connected system like water, from an excessively long time to a feasible value.

Ethanol preconditioning of rat cerebellar cultures targets NMDA receptors to the synapse and enhances peroxiredoxin 2 expression.

Epidemiological studies indicate that light-moderate alcohol (ethanol) consumers tend to have reduced risks of cognitive impairment and progression to dementia during aging. Exploring possible mechanisms, we previously found that moderate ethanol preconditioning (MEP, 20-30mM) of rat brain cultures for several days instigated neuroprotection against ß-amyloid peptides. Our biochemical evidence implicated the NMDA receptor (NMDAR) as a potential neuroprotective "sensor", specifically via synaptic NMDAR signaling. It remains unclear how ethanol modulates the receptor and its downstream targets to engender neuroprotection. Here we confirm with deconvolution microscopy that MEP of rat mixed cerebellar cultures robustly increases synaptic NMDAR localization. Phospho-activation of the non-receptor tyrosine kinases Src and Pyk2, known to be linked to synaptic NMDAR, is also demonstrated. Additionally, the preconditioning enhances levels of an antioxidant protein, peroxiredoxin 2 (Prx2), reported to be downstream of synaptic NMDAR signaling, and NMDAR antagonism with memantine (earlier found to abrogate MEP neuroprotection) blocks the Prx2 elevations. To further link Prx2 with antioxidant-based neuroprotection, we circumvented the ethanol preconditioning-NMDAR pathway by pharmacologically increasing Prx2 with the naturally-occurring cruciferous compound, 3H-1,2-dithiole-3-thione (D3T). Thus, D3T pretreatment elevated Prx2 expression to a similar extent as MEP, while concomitantly preventing ß-amyloid neurotoxicity; D3T also protected the cultures from hydrogen peroxide toxicity. The findings support a mechanism that couples synaptic NMDAR signaling, Prx2 expression and augmented antioxidant defenses in ethanol preconditioning-induced neuroprotection. That this mechanism can be emulated by a cruciferous vegetable constituent suggests that such naturally-occurring "neutraceuticals" may be useful in therapy for oxidative stress-related dementias.

Approximating CCSD(T) Nuclear Magnetic Shielding Calculations Using Composite Methods.

A series of composite method approximations for the computationally efficient calculation of NMR shieldings has been developed. These approximations utilize basis sets from the pcS-n series, which is shown to converge rapidly toward experimental gas-phase shieldings at CCSD(T). The possibility of using HF, B3LYP, KT3, or MP2 shieldings to approximate results at CCSD(T) was then examined. It was determined that using HF in conjunction with MP2 significantly reduces the CPU time of calculations while having a minimal impact on the accuracy of the predicted shieldings.

H2 Adsorption in a Porous Crystal: Accurate First-Principles Quantum Simulation.

A general method is presented for constructing, from ab initio quantum chemistry calculations, the potential energy surface (PES) for H2 absorbed in a porous crystalline material. The method is illustrated for the metal-organic framework material MOF-5. Rigid body quantum diffusion Monte Carlo simulations are used in the construction of the PES and to evaluate the quantum ground state of H2 in MOF-5, the zero-point energy, and the enthalpy of adsorption at 0 K.

Calculating nuclear magnetic resonance shieldings using systematic molecular fragmentation by annihilation.

SMFA was used to calculate NMR shieldings in a test set of 15 molecules. Level 4 fragments were found to yield satisfactory results when hydrogen bonding was included in the calculations. The utility of additional long range corrections was also investigated. It was found that with hydrogen bonding already included, ab initio long range corrections were not necessary. Instead, inclusion of the McConnell correction for fragments was found to be sufficient. With these parameters the algorithm produces MADs of 0.046, 0.26, 0.24 and 1.04 ppm for hydrogens, carbons, nitrogens and oxygens respectively.

Molecular forces, geometries, and frequencies by systematic molecular fragmentation including embedded charges.

The accuracy of energies, energy gradients, and hessians evaluated by systematic molecular fragmentation is examined for a wide range of neutral molecules, zwitterions, and ions. A protocol is established that may employ embedded charges in conjunction with fragmentation to provide accurate evaluation of minimum energy geometries and vibrational frequencies in an automated procedure.

Neuroinflammation and neurodegeneration in adult rat brain from binge ethanol exposure: abrogation by docosahexaenoic acid.

Evidence that brain edema and aquaporin-4 (AQP4) water channels have roles in experimental binge ethanol-induced neurodegeneration has stimulated interest in swelling/edema-linked neuroinflammatory pathways leading to oxidative stress. We report here that neurotoxic binge ethanol exposure produces comparable significant effects in vivo and in vitro on adult rat brain levels of AQP4 as well as neuroinflammation-linked enzymes: key phospholipase A2 (PLA2) family members and poly (ADP-ribose) polymerase-1 (PARP-1). In adult male rats, repetitive ethanol intoxication (3 gavages/d for 4 d, ∼ 9 g/kg/d, achieving blood ethanol levels ∼ 375 mg/dl; "Majchrowicz" model) significantly increased AQP4, Ca+2-dependent PLA2 GIVA (cPLA2), phospho-cPLA2 GIVA (p-cPLA2), secretory PLA2 GIIA (sPLA2) and PARP-1 in regions incurring extensive neurodegeneration in this model--hippocampus, entorhinal cortex, and olfactory bulb--but not in two regions typically lacking neurodamage, frontal cortex and cerebellum. Also, ethanol reduced hippocampal Ca+2-independent PLA2 GVIA (iPLA2) levels and increased brain "oxidative stress footprints" (4-hydroxynonenal-adducted proteins). For in vitro studies, organotypic cultures of rat hippocampal-entorhinocortical slices of adult age (∼ 60 d) were ethanol-binged (100 mM or ∼ 450 mg/dl) for 4 d, which augments AQP4 and causes neurodegeneration (Collins et al. 2013). Reproducing the in vivo results, cPLA2, p-cPLA2, sPLA2 and PARP-1 were significantly elevated while iPLA2 was decreased. Furthermore, supplementation with docosahexaenoic acid (DHA; 22:6n-3), known to quell AQP4 and neurodegeneration in ethanol-treated slices, blocked PARP-1 and PLA2 changes while counteracting endogenous DHA reduction and increases in oxidative stress footprints (3-nitrotyrosinated proteins). Notably, the PARP-1 inhibitor PJ-34 suppressed binge ethanol-dependent neurodegeneration, indicating PARP upstream involvement. The results with corresponding models support involvement of AQP4- and PLA2-associated neuroinflammatory pro-oxidative pathways in the neurodamage, with potential regulation by PARP-1 as well. Furthermore, DHA emerges as an effective inhibitor of these binge ethanol-dependent neuroinflammatory pathways as well as associated neurodegeneration in adult-age brain.

The combined fragmentation and systematic molecular fragmentation methods.

Conspectus Chemistry, particularly organic chemistry, is mostly concerned with functional groups: amines, amides, alcohols, ketones, and so forth. This is because the reactivity of molecules can be categorized in terms of the reactions of these functional groups, and by the influence of other adjacent groups in the molecule. These simple truths ought to be reflected in the electronic structure and electronic energy of molecules, as reactivity is determined by electronic structure. However, sophisticated ab initio quantum calculations of the molecular electronic energy usually do not make these truths apparent. In recent years, several computational chemistry groups have discovered methods for estimating the electronic energy as a sum of the energies of small molecular fragments, or small sets of groups. By decomposing molecules into such fragments of adjacent functional groups, researchers can estimate the electronic energy to chemical accuracy; not just qualitative trends, but accurate enough to understand reactivity. In addition, this has the benefit of cutting down on both computational time and cost, as the necessary calculation time increases rapidly with an increasing number of electrons. Even with steady advances in computer technology, progress in the study of large molecules is slow. In this Account, we describe two related "fragmentation" methods for treating molecules, the combined fragmentation method (CFM) and systematic molecular fragmentation (SMF). In addition, we show how we can use the SMF approach to estimate the energy and properties of nonconducting crystals, by fragmenting the periodic crystal structure into relatively small pieces. A large part of this Account is devoted to simple overviews of how the methods work. We also discuss the application of these approaches to calculating reactivity and other useful properties, such as the NMR and vibrational spectra of molecules and crystals. These applications rely on the ability of these fragmentation methods to accurately estimate derivatives of the molecular and crystal energies. Finally, to provide some common applications of CFM and SMF, we present some specific examples of energy calculations for moderately large molecules. For computational chemists, this fragmentation approach represents an important practical advance. It reduces the computer time required to estimate the energies of molecules so dramatically, that accurate calculations of the energies and reactivity of very large organic and biological molecules become feasible.

Application of best practice approaches for designing decision support tools: the preparatory education about clinical trials (PRE-ACT) study.

OBJECTIVE: This article describes the rigorous development process and initial feedback of the PRE-ACT (Preparatory Education About Clinical Trials) web-based- intervention designed to improve preparation for decision making in cancer clinical trials. METHODS: The multi-step process included stakeholder input, formative research, user testing and feedback. Diverse teams (researchers, advocates and developers) participated including content refinement, identification of actors, and development of video scripts. Patient feedback was provided in the final production period and through a vanguard group (N=100) from the randomized trial. RESULTS: Patients/advocates confirmed barriers to cancer clinical trial participation, including lack of awareness and knowledge, fear of side effects, logistical concerns, and mistrust. Patients indicated they liked the tool's user-friendly nature, the organized and comprehensive presentation of the subject matter, and the clarity of the videos. CONCLUSION: The development process serves as an example of operationalizing best practice approaches and highlights the value of a multi-disciplinary team to develop a theory-based, sophisticated tool that patients found useful in their decision making process. Practice implications Best practice approaches can be addressed and are important to ensure evidence-based tools that are of value to patients and supports the usefulness of a process map in the development of e-health tools.

Alcohol, phospholipase A2-associated neuroinflammation, and ω3 docosahexaenoic acid protection.

Chronic alcohol (ethanol) abuse causes neuroinflammation and brain damage that can give rise to alcoholic dementia. Insightfully, Dr. Albert Sun was an early proponent of oxidative stress as a key factor in alcoholism-related brain deterioration. In fact, oxidative stress has proven to be critical to the hippocampal and temporal cortical neurodamage resulting from repetitive "binge" alcohol exposure in adult rat models. Although the underlying mechanisms are uncertain, our immunoelectrophoretic and related assays in binge alcohol experiments in vivo (adult male rats) and in vitro (rat organotypic hippocampal-entorhinal cortical slice cultures) have implicated phospholipase A(2) (PLA(2))-activated neuroinflammatory pathways, release of pro-oxidative arachidonic acid (20:4 ω6), and elevated oxidative stress adducts (i.e., 4-hydroxynonenal-protein adducts). Also, significantly increased by the binge alcohol treatments was aquaporin-4 (AQP4), a water channel enriched in astrocytes that, when augmented, may trigger brain (esp. cellular) edema and neuroinflammation; of relevance, glial swelling is known to provoke increased PLA(2) activities or levels. Concomitant with PLA(2) activation, the results have further implicated binge alcohol-elevated poly (ADP-ribose) polymerase-1 (PARP-1), an oxidative stress-responsive DNA repair enzyme linked to parthanatos, a necrotic-like neuronal death process. Importantly, supplementation of the brain slice cultures with docosahexaenoic acid (22:6 ω3) exerted potent suppression of the induced changes in PLA(2) isoforms, AQP4, PARP-1 and oxidative stress footprints, and prevention of the binge alcohol neurotoxicity, by as yet unknown mechanisms. These neuroinflammatory findings from our binge alcohol studies and supportive rat binge studies in the literature are reviewed.

Systematic Study of Locally Dense Basis Sets for NMR Shielding Constants.

This paper presents a systematic study of partitioning schemes for locally dense basis sets in the context of NMR shielding calculations. The partitionings explored were based exclusively on connectivity and utilized the basis sets from the pcS-n series. Deviations from pcS-4 shieldings were calculated for a set of 28 organic molecules at the HF, B3LYP, and KT3 levels of theory, with the primary goal being the determination of an efficient scheme that achieves maximal deviations of 0.1 ppm for (1)H and 1 ppm for (13)C. Both atom based and group based divisions of basis sets were examined, with the latter providing the most promising results. It is demonstrated that for the systems studied, at least pcS-1 is required for all parts of the molecule. This, coupled with pcS-3 on the group of interest and pcS-2 on the adjacent groups, is sufficient to achieve the desired level of accuracy at a minimal computational expense. In addition, the suitability of the pcS-n basis sets for post-SCF methods was confirmed through a comparison with other standard basis sets at the MP2 level.

Sharing behavioral data through a grid infrastructure using data standards.

OBJECTIVE: In an effort to standardize behavioral measures and their data representation, the present study develops a methodology for incorporating measures found in the National Cancer Institute's (NCI) grid-enabled measures (GEM) portal, a repository for behavioral and social measures, into the cancer data standards registry and repository (caDSR). METHODS: The methodology consists of four parts for curating GEM measures into the caDSR: (1) develop unified modeling language (UML) models for behavioral measures; (2) create common data elements (CDE) for UML components; (3) bind CDE with concepts from the NCI thesaurus; and (4) register CDE in the caDSR. RESULTS: UML models have been developed for four GEM measures, which have been registered in the caDSR as CDE. New behavioral concepts related to these measures have been created and incorporated into the NCI thesaurus. Best practices for representing measures using UML models have been utilized in the practice (eg, caDSR). One dataset based on a GEM-curated measure is available for use by other systems and users connected to the grid. CONCLUSIONS: Behavioral and population science data can be standardized by using and extending current standards. A new branch of CDE for behavioral science was developed for the caDSR. It expands the caDSR domain coverage beyond the clinical and biological areas. In addition, missing terms and concepts specific to the behavioral measures addressed in this paper were added to the NCI thesaurus. A methodology was developed and refined for curation of behavioral and population science data.