Variable Cadence Gait Training Outcomes Using Rhythmic Auditory Stimulation Embedded in Older Adults' Preferred Music.

Older adults must have the ability to walk at variable speeds/distances to meet community demands. This single group pre-post test study's purposes were to examine if actual cadences after 7 weeks of rhythmic auditory stimulation gait training matched target cadences, improved walking distance, duration, velocity, maximum cadence, balance, enjoyment, and/or changed spatial/temporal gait parameters. Fourteen female adults (72.6 ± 4.4 years) participated in 14 sessions, while variable cadences were progressively introduced. Eleven older adult responders walked faster (3.8 steps/min) than one target cadence (-10% pace) while matching the target cadences for the other paces when walking with rhythmic auditory stimulation. Two nonresponders walked near their baseline cadence with little variability while one walked at faster cadences; all three did not appear to adjust to the beat of the music. After training, participants increased their walking distance, 90.8 ± 46.5 m; t(1, 13) = -7.3; p ≤ .005, velocity, 0.36 ± 0.15 m/s; t(1, 40) = -15.4; p < .001, and maximum cadence, 20.6 ± 9.1 steps/min; t(1, 40) = -14.6; p < .001; changes exceeded minimal clinically important differences. Twelve of 14 expressed enjoyment. Walk with rhythmic auditory stimulation training is a promising activity for older adults, which may translate to an individual's ability to adapt walking speeds to various community demands.

Met35 Oxidation Hinders Aß25-35 Peptide Aggregation within the Dimyristoylphosphatidylcholine Bilayer.

Using all-atom explicit solvent replica exchange molecular dynamics simulations, we studied the aggregation of oxidized (ox) Aß25-35 peptides into dimers mediated by the zwitterionic dimyristoylphosphatidylcholine (DMPC) lipid bilayer. By comparing oxAß25-35 aggregation with that observed for reduced and phosphorylated Aß25-35 peptides, we elucidated plausible impact of post-translational modifications on cytotoxicity of Aß peptides involved in Alzheimer's disease. We found that Met35 oxidation reduces helical propensity in oxAß25-35 peptides bound to the lipid bilayer and enhances backbone fluctuations. These factors destabilize the wild-type head-to-tail dimer interface and lower the aggregation propensity. Met35 oxidation diversifies aggregation pathways by adding monomeric species to the bound conformational ensemble. The oxAß25-35 dimer becomes partially expelled from the DMPC bilayer and as a result inflicts limited disruption to the bilayer structure compared to wild-type Aß25-35. Interestingly, the effect of Ser26 phosphorylation is largely opposite, as it preserves the wild-type head-to-tail aggregation interface and strengthens, not weakens, aggregation propensity. The differing effects can be attributed to the sequence locations of these post-translational modifications, since in contrast to Ser26 phosphorylation, Met35 oxidation directly affects the wild-type C-terminal aggregation interface. A comparison with experimental data is provided.

Partitioning of Aß Peptide Fragments into Blood-Brain Barrier Mimetic Bilayer.

We used all-atom replica-exchange umbrella sampling molecular dynamics simulations to investigate the partitioning of the charged tetrapeptide KLVF and its neutral apolar counterpart VVIA into the blood-brain barrier (BBB)-mimetic bilayer. Our findings allowed us to reconstruct the partitioning mechanism for these two Aß peptide fragments. Despite dissimilar sequences, their permeation shares significant common features. Computations of free energies and permeabilities show that partitioning of both peptides is highly unfavorable, ruling out passive transport. The peptides experience multiple rotational transitions within the bilayer and typically cause considerable lipid disorder and bilayer thinning. Near the bilayer midplane, they lose almost entirely their solvation shell and the interactions with the lipid headgroups. The peptides cause complex reorganization within the proximal bilayer region. Upon insertion, they induce striking cholesterol influx reversed by its depletion and the influx of DMPC when the peptides reach the midplane. The differences in partitioning mechanisms are due to the much higher polarity of KLVF peptide, the permeation of which is more unfavorable and which exclusively assumes vertical orientations within the bilayer. In contrast, VVIA positions itself flat between the leaflets, causing minor disorder and even thickening of the BBB-mimetic bilayer. Due to the high density of the cholesterol-rich BBB bilayer, the unfavorable work associated with the peptide insertion provides a significant, but not dominant, contribution to the partition free energy, which is still governed by dehydration and loss of peptide-headgroup interactions. Comparison with experiments indicates that KLVF and VVIA permeation is similar to that of proline tetrapeptide, mannitol, or cimetidine, all of which exhibit no passive transport.

Phosphorylation Promotes Aß25-35 Peptide Aggregation within the DMPC Bilayer.

The consequences of phosphorylation of the Aß25-35 peptide at the position Ser26 on its aggregation have not been examined. To investigate them, we performed all-atom replica exchange simulations probing the binding of phosphorylated Aß25-35 (pAß25-35) peptides to the dimyristoyl phosphatidylcholine (DMPC) bilayer and their subsequent aggregation. As a control, we used our previous study of unmodified peptides. We found that phosphorylation moderately reduces the helical propensity in pAß25-35 and its binding affinity to the DMPC bilayer. Phosphorylation preserves the bimodal binding observed for unmodified Aß25-35, which features a preferred inserted state and a less probable surface bound state. Phosphorylation also retains the inserted dimer with a head-to-tail helical aggregation interface as the most thermodynamically stable state. Importantly, this post-translation modification strengthens interpeptide interactions by adding a new aggregation "hot spot" created by cross-bridging phosphorylated Ser26 with water, cationic ions, or Lys28. The cross-bridging constitutes the molecular mechanism behind most structural phosphorylation effects. In addition, phosphorylation eliminates pAß25-35 monomers and diversifies the pool of aggregated species. As a result, it changes the binding and aggregation mechanism by multiplying pathways leading to stable inserted dimers. These findings offer a plausible molecular rationale for experimental observations, including enhanced production of low molecular weight oligomers and cytotoxicity of phosphorylated Aß peptides.

Partitioning of Benzoic Acid into 1,2-Dimyristoyl-sn-glycero-3-phosphocholine and Blood-Brain Barrier Mimetic Bilayers.

Using an all-atom explicit water model and replica exchange umbrella sampling simulations, we investigated the molecular mechanisms of benzoic acid partitioning into two model lipid bilayers. The first was formed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids, whereas the second was composed of an equimolar mixture of DMPC, 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine, palmitoylsphingomyelin, and cholesterol to constitute a blood-brain barrier (BBB) mimetic bilayer. Comparative analysis of benzoic acid partitioning into the two bilayers has revealed qualitative similarities. Partitioning into the DMPC and BBB bilayers is thermodynamically favorable although insertion into the former lowers the free energy of benzoic acid by approximately an additional 1 kcal mol-1. The partitioning energetics for the two bilayers is also largely similar based on the balance of benzoic acid interactions with apolar fatty acid tails, polar lipid headgroups, and water. In both bilayers, benzoic acid retains a considerable number of residual water molecules until reaching the bilayer midplane where it experiences nearly complete dehydration. Upon insertion into the bilayers, benzoic acid undergoes several rotations primarily determined by the interactions with the lipid headgroups. Nonetheless, in addition to the depth of the free energy minimum, the BBB bilayer differs from the DMPC counterpart by a much deeper location of the free energy minimum and the appearance of a high free energy barrier and positioning of benzoic acid near the midplane. Furthermore, DMPC and BBB bilayers exhibit different structural responses to benzoic acid insertion. Taken together, the BBB mimetic bilayer is preferable for an accurate description of benzoic acid partitioning.

Three Popular Force Fields Predict Consensus Mechanism of Amyloid ß Peptide Binding to the Dimyristoylgylcerophosphocholine Bilayer.

Using all-atom explicit water replica-exchange molecular dynamics simulations, we examined the impact of three popular force fields (FF) on the equilibrium binding of Aß10-40 peptide to the dimyristoylgylcerophosphocholine (DMPC) bilayer. The comparison included CHARMM22 protein FF with CHARMM36 lipid FF (C22), CHARMM36m protein FF with CHARMM36 lipid FF (C36), and Amber14SB protein FF with Lipid14 lipid FF (A14). Analysis of Aß10-40 binding to the DMPC bilayer in three FFs revealed a consensus binding mechanism. Its main features include (i) a stable helical structure in the bound peptide, (ii) insertion of the C-terminus and, in part, the central hydrophobic cluster into the bilayer hydrophobic core, (iii) considerable thinning of the DMPC bilayer beneath the bound peptide coupled with significant drop in bilayer density, and (iv) a strong disordering in the DMPC fatty acid tails. Although the three FFs diverge on many details concerning Aß and bilayer conformational ensembles, these discrepancies do not offset the features of the consensus binding mechanism. We compared our findings with other FF evaluations and proposed that an agreement between C22, C36, and A14 is a consequence of a strong ordering effect created by polar-apolar interface in the lipid bilayer. By comparing the consensus Aß binding mechanism with experimental data, we surmise that the three tested FFs largely correctly capture the interactions of Aß peptides with the DMPC lipid bilayer.

Extracts of Common Pesticidal Plants Increase Plant Growth and Yield in Common Bean Plants.

Common bean (Phaseolus vulgaris) is an important food and cash crop in many countries. Bean crop yields in sub-Saharan Africa are on average 50% lower than the global average, which is largely due to severe problems with pests and diseases as well as poor soil fertility exacerbated by low-input smallholder production systems. Recent on-farm research in eastern Africa has shown that commonly available plants with pesticidal properties can successfully manage arthropod pests. However, reducing common bean yield gaps still requires further sustainable solutions to other crop provisioning services such as soil fertility and plant nutrition. Smallholder farmers using pesticidal plants have claimed that the application of pesticidal plant extracts boosts plant growth, potentially through working as a foliar fertiliser. Thus, the aims of the research presented here were to determine whether plant growth and yield could be enhanced and which metabolic processes were induced through the application of plant extracts commonly used for pest control in eastern Africa. Extracts from Tephrosia vogelii and Tithonia diversifolia were prepared at a concentration of 10% w/v and applied to potted bean plants in a pest-free screen house as foliar sprays as well as directly to the soil around bean plants to evaluate their contribution to growth, yield and potential changes in primary or secondary metabolites. Outcomes of this study showed that the plant extracts significantly increased chlorophyll content, the number of pods per plant and overall seed yield. Other increases in metabolites were observed, including of rutin, phenylalanine and tryptophan. The plant extracts had a similar effect to a commercially available foliar fertiliser whilst the application as a foliar spray was better than applying the extract to the soil. These results suggest that pesticidal plant extracts can help overcome multiple limitations in crop provisioning services, enhancing plant nutrition in addition to their established uses for crop pest management.

Use of Nanotrap particles for the capture and enrichment of Zika, chikungunya and dengue viruses in urine.

Nanotrap® (NT) particles are hydrogel microspheres developed for target analyte separation and discovery applications. NT particles consist of cross-linked N-isopropylacrylamide (NIPAm) copolymers that are functionalized with a variety of chemical affinity baits to enable broad-spectrum collection and retention of target proteins, nucleic acids, and pathogens. NT particles have been previously shown to capture and enrich arboviruses including Rift Valley fever and Venezuelan equine encephalitis viruses. Yet, there is still a need to enhance the detection ability for other re-emerging viruses such as Zika (ZIKV), chikungunya (CHIKV), and dengue (DENV) viruses. In this study, we exploited NT particles with different affinity baits, including cibacron blue, acrylic acid, and reactive red 120, to evaluate their capturing and enrichment capability for ZIKV, DENV and CHIKV in human fluids. Our results demonstrate that CN1030, a NT particle conjugated with reactive red 120, can recover between 8-16-fold greater genomic copies of ZIKV, CHIKV and DENV in virus spiked urine samples via RT-qPCR, superior to the other chemical baits. Also, we observed that CN1030 simultaneously enriched ZIKV, CHIKV and DENV in co-infection-based settings and could stabilize ZIKV, but not CHIKV infectivity in saliva spiked samples. CN1030 enriched viral detection at various viral concentrations, with significant enhancement observed at viral titers as low as 100 PFU/mL for ZIKV and 10 PFU/mL for CHIKV. The detection of ZIKV was further enhanced with NT particles by processing of larger volume urine samples. Furthermore, we developed a magnetic NT particle, CN3080, based on the same backbone of CN1030, and demonstrated that CN3080 could also capture and enrich ZIKV and CHIKV in a dose-dependent manner. Finally, in silico docking predictions support that the affinity between reactive red 120 and ZIKV or CHIKV envelope proteins appeared to be greater than acrylic acid. Overall, our data show that NT particles along with reactive red 120 can be utilized as a pre-processing technology for enhancement of detecting febrile-illness causing viruses.

Do Cholesterol and Sphingomyelin Change the Mechanism of Aß25-35 Peptide Binding to Zwitterionic Bilayer?

Using replica exchange with solute tempering all-atom molecular dynamics, we studied the equilibrium binding of Aß25-35 peptide to the ternary bilayer composed of an equimolar mixture of dimyristoylphosphatidylcholine (DMPC), N-palmitoylsphingomyelin (PSM), and cholesterol. Binding of the same peptide to the pure DMPC bilayer served as a control. Due to significant C-terminal hydrophobic moment, binding to the ternary and DMPC bilayers promotes helical structure in the peptide. For both bilayers a polarized binding profile is observed, in which the N-terminus anchors to the bilayer surface, whereas the C-terminus alternates between unbound and inserted states. Both ternary and DMPC bilayers feature two Aß25-35 bound states, surface bound, S, and inserted, I, separated by modest free energy barriers. Experimental data are in agreement with our results but indicate that cholesterol impact is Aß fragment dependent. For Aß25-35, we predict that its binding mechanism is independent of the inclusion of PSM and cholesterol into the bilayer.

De novo aggregation of Alzheimer's Aß25-35 peptides in a lipid bilayer.

A potential mechanism of cytotoxicity attributed to Alzheimer's Aß peptides postulates that their aggregation disrupts membrane structure causing uncontrollable permeation of Ca2+ ions. To gain molecular insights into these processes, we have performed all-atom explicit solvent replica exchange with solute tempering molecular dynamics simulations probing aggregation of the naturally occurring Aß fragment Aß25-35 within the DMPC lipid bilayer. To compare the impact produced on the bilayer by Aß25-35 oligomers and monomers, we used as a control our previous simulations, which explored binding of Aß25-35 monomers to the same bilayer. We found that compared to monomeric species aggregation results in much deeper insertion of Aß25-35 peptides into the bilayer hydrophobic core causing more pronounced disruption in its structure. Aß25-35 peptides aggregate by incorporating monomer-like structures with stable C-terminal helix. As a result the Aß25-35 dimer features unusual helix head-to-tail topology supported by a parallel off-registry interface. Such topology affords further growth of an aggregate by recruiting additional peptides. Free energy landscape reveals that inserted dimers represent the dominant equilibrium state augmented by two metastable states associated with surface bound dimers and inserted monomers. Using the free energy landscape we propose the pathway of Aß25-35 binding, aggregation, and insertion into the lipid bilayer.

Methionine Oxidation Changes the Mechanism of Aß Peptide Binding to the DMPC Bilayer.

Using all-atom explicit solvent replica exchange molecular dynamics simulations with solute tempering, we study the effect of methionine oxidation on Aß10-40 peptide binding to the zwitterionic DMPC bilayer. By comparing oxidized and reduced peptides, we identified changes in the binding mechanism caused by this modification. First, Met35 oxidation unravels C-terminal helix in the bound peptides. Second, oxidation destabilizes intrapeptide interactions and expands bound peptides. We explain these outcomes by the loss of amphiphilic character of the C-terminal helix due to oxidation. Third, oxidation "polarizes" Aß binding to the DMPC bilayer by strengthening the interactions of the C-terminus with lipids while largely releasing the rest of the peptide from bilayer. Fourth, in contrast to the wild-type peptide, oxidized Aß induces significantly smaller bilayer thinning and drop in lipid density within the binding footprint. These observations are the consequence of mixing oxidized peptide amino acids with lipids promoted by enhanced Aß conformational fluctuations. Fifth, methionine oxidation reduces the affinity of Aß binding to the DMPC bilayer by disrupting favorable intrapeptide interactions upon binding, which offset the gains from better hydration. Reduced binding affinity of the oxidized Aß may represent the molecular basis for its reduced cytotoxicity.

Molecular Dynamics Investigation of the Ternary Bilayer Formed by Saturated Phosphotidylcholine, Sphingomyelin, and Cholesterol.

Using the all-atom CHARMM36 force field, we have performed molecular dynamics simulations of the equimolar ternary dimyristoylphosphatidylcholine (DMPC)/ N-palmitoylsphingomyelin (PSM)/cholesterol bilayer. Analysis of its structural and kinetic properties has led us to the following conclusions. First, the DMPC/PSM/cholesterol bilayer features favorable interactions of cholesterol with DMPC and, particularly, PSM lipids, which are supported by hydrogen bonds. In contrast, the interactions between cholesterol molecules are strongly suppressed. Further analysis shows that about 60% of PSM molecules form hydrogen bonds with other PSM or cholesterol molecules and, to a lesser degree, with DMPC lipids. Second, local lipid packing around PSM molecules favors parallel or antiparallel alignments, resulting in the appearance of large anisotropic chain-like clusters formed by PSM lipids. In contrast, the distribution of DMPC lipids is closer to ideal, whereas the cholesterol distribution is sharply shifted toward small clusters or isolated molecules. Third, intermolecular interactions and mismatch in fatty acid tail lengths significantly slow down PSM rotational relaxation compared to that for DMPC, and PSM, but not DMPC lipids, tend to combine axial rotation with wobbling. Fourth, the analysis of cholesterol hydration indicates that lipid headgroups at most block about 30% of water molecules from reaching cholesterol, hinting at limited applicability of the umbrella model. Finally, we show that PSM and DMPC lipids predominantly exist in two equally probable conformational states, with and without a kink in their fatty acid tails. The appearance of these states is linked to the impact of cholesterol. Comparisons with previous studies allow us to delineate contributions of cholesterol, PSM, and DMPC to bilayer properties.

Binding of Cytotoxic Aß25-35 Peptide to the Dimyristoylphosphatidylcholine Lipid Bilayer.

Aß25-35 is a short, cytotoxic, and naturally occurring fragment of the Alzheimer's Aß peptide. To map the molecular mechanism of Aß25-35 binding to the zwitterionic dimyristoylphosphatidylcholine (DMPC) bilayer, we have performed replica exchange with solute tempering molecular dynamics simulations using all-atom explicit membrane and water models. Consequences of sequence truncation on the binding mechanism have been measured by utilizing as a control our previous simulations probing binding of the longer peptide Aß10-40 to the same bilayer. The most intriguing feature of Aß25-35 binding to the DMPC bilayer is a coexistence of two bound states with strikingly different characteristics: a dominant surface-bound state and a less stable inserted state. In the surface-bound state, the peptide samples extended conformations, in which its unbound C-terminal is pointed away from the bilayer. In contrast, in the inserted state, the C-terminal resides deep in the bilayer hydrophobic core. In both states, the N-terminal remains anchored to the bilayer. Free energy landscape analysis reveals that the two states are separated by a moderate barrier, suggesting that Aß25-35 monomer may frequently interconvert between them. The net effect of Aß25-35 binding is a minor impact on the bilayer structure, which contrasts with the considerable bilayer perturbations induced by a longer Aß10-40 peptide penetrating deep into the bilayer core. Therefore, we conclude that the binding mechanisms of Aß25-35 and Aß10-40 peptides are different. Potential implications of our results for Aß25-35 cytotoxicity are discussed. A comparison of experimental data with our findings reveals a good agreement.

Role of the type I tumor necrosis factor receptor in inflammation-associated olfactory dysfunction.

BACKGROUND: To understand mechanisms of human olfactory dysfunction in chronic rhinosinusitis, an inducible olfactory inflammation (IOI) model has been utilized to chronically express inflammatory cytokines locally, resulting in neuronal loss, diminished odorant responses, and repressed olfactory regeneration. Knockout of the minor tumor necrosis factor α receptor 2 (TNFR2) was previously shown to partially rescue these olfactory changes. The purpose of current study was to investigate the role of the major TNF receptor, TNFR1, in chronic olfactory inflammation. METHODS: Two experimental groups of mice were studied: TNFR1 knockout in IOI background and TNFR1 knockout with allergen-induced inflammation. Olfactory function was assayed by electro-olfactogram (EOG), and olfactory tissue was processed for histology and immunohistochemical staining. RESULTS: TNF-α was dramatically induced in IOI-TNFR1 knockout mice, but the olfactory epithelium did not show inflammation. EOG responses were normal after either 2 or 8 weeks of TNF-α expression. Ovalbumin-sensitized TNFR1 knockout mice developed markedly diminished eosinophilic inflammatory infiltration. CONCLUSION: Genetic deletion of TNFR1 completely blocks TNF-α-induced inflammation and reduces allergen-induced inflammation. Preserved EOG responses suggest a TNFR1-dependent mechanism of TNF-α-induced olfactory neuron dysfunction.

Does Replica Exchange with Solute Tempering Efficiently Sample Aß Peptide Conformational Ensembles?

We have applied replica exchange with solute tempering (REST) molecular dynamics to study a short fragment of the Aß peptide, Aß25-35, in water and a much larger system incorporating two Aß10-40 peptides binding to the zwitterionic dimyristoylphosphatidylcholine (DMPC) bilayer. As a control, we used traditional replica exchange molecular dynamics (REMD) applied to the same systems. Our objective was to assess the practical utility of REST simulations. Taken together, our results suggest four conclusions. First, compared to REMD, the number of replicas in REST simulations can be reduced four to five times without affecting the temperature range or compromising an efficient random walk of REST replicas over temperatures. Second, although overall REST produces much fewer conformational states than REMD, there is no substantial difference in the collection of unique states for the wild-type replica in REST and REMD, especially for the system featuring Aß peptides binding to the lipid bilayer. Third, we performed a thorough comparison of REST and REMD equilibrium conformational ensembles, including thermal averages and probability distributions. REST reproduces REMD data extremely well for the system of Aß peptides binding to the DMPC lipid bilayer. The agreement between REST and REMD equilibrium sampling of Aß25-35 in water is less perfect, but it improves with addition of new REST simulations. Surprisingly, REST demonstrates much better convergence for the system featuring ordered peptides binding to lipid bilayer rather than for a small unstructured peptide solvated in water. Fourth, REST delivers its full computational advantage over REMD when applied to peptides interacting with lipid bilayers. For peptides solvated in water, REST does not appear to offer computational gain but may make replica simulations practically feasible due to a lower requirement for parallel computing environments. Our study is expected to facilitate wider application of REST in biomolecular simulations.