Molecular analysis of point-of-use municipal drinking water microbiology

Little is known about the nature of the microbiology in tap waters delivered to consumers via public drinking water distribution systems (DWDSs). In order to establish a broader understanding of the microbial complexity of public drinking waters we sampled tap water from seventeen different cities between the headwaters of the Arkansas River and the mouth of the Mississippi River and determined the bacterial compositions by pyrosequencing small subunit rRNA genes. Nearly 98% of sequences observed among all systems fell into only 5 phyla: Proteobacteria (35%), Cyanobacteria (29%, including chloroplasts), Actinobacteria (24%, of which 85% were Mycobacterium spp.), Firmicutes (6%), and Bacteroidetes (3.4%). The genus Mycobacterium was the most abundant taxon in the dataset, detected in 56 of 63 samples (16 of 17 cities). Among the more rare phylotypes, considerable variation was observed between systems, and was sometimes associated with the type of source water, the type of disinfectant, or the concentration of the environmental pollutant nitrate. Abundant taxa (excepting Cyanobacteria and chloroplasts) were generally similar from system to system, however, regardless of source water type or local land use. The observed similarity among the abundant taxa between systems may be a consequence of the selective influence of chlorine-based disinfection and the common local environments of DWDS and premise plumbing pipes.

Self-assembly of chiral tubules

The efficient and controlled assembly of complex structures from macromolecular building blocks is a critical open question in both biological systems and nanoscience. Using molecular dynamics simulations we study the self-assembly of tubular structures from model macromolecular monomers with multiple binding sites on their surfaces [Cheng et al., Soft Matter, 2012, 8, 5666-5678]. In this work we add chirality to the model monomer and a lock-and-key interaction. The self-assembly of free monomers into tubules yields a pitch value that often does not match the chirality of the monomer (including achiral monomers). We show that this mismatch occurs because of a twist deformation that brings the lateral interaction sites into alignment when the tubule pitch differs from the monomer chirality. The energy cost for this deformation is small as the energy distributions substantially overlap for small differences in the pitch and chirality. In order to control the tubule pitch by preventing the twist deformation, the interaction between the vertical surfaces must be increased without resulting in kinetically trapped structures. For this purpose, we employ lock-and-key interactions and obtain good control of the self-assembled tubule pitch. These results explain some fundamental features of microtubules. The vertical interaction strength is larger than the lateral in microtubules because this yields a controlled assembly of tubules with the proper pitch. We also generally find that the control of the assembly into tubules is difficult, which explains the wide range of pitch values and protofilament numbers observed in microtubule assembly.

Effects of triple antioxidant therapy on measures of cardiovascular autonomic neuropathy and on myocardial blood flow in type 1 diabetes: a randomised controlled trial

AIMS/HYPOTHESIS

We evaluated the effects of a combination triple antioxidant therapy on measures of cardiovascular autonomic neuropathy (CAN) and myocardial blood flow (MBF) in patients with type 1 diabetes.

METHODS

This was a randomised, parallel, placebo-controlled trial. Participants were allocated to interventions by sequentially numbered, opaque, sealed envelopes provided to the research pharmacist. All participants and examiners were masked to treatment allocation. Participants were evaluated by cardiovascular autonomic reflex testing, positron emission tomography with [(11)C]meta-hydroxyephedrine ([(11)C]HED) and [(13)N]ammonia, and adenosine stress testing. Markers of oxidative stress included 24 h urinary F2-isoprostanes. Diabetic peripheral neuropathy (DPN) was evaluated by symptoms, signs, electrophysiology and intra-epidermal nerve fibre density. Randomised participants included 44 eligible adults with type 1 diabetes and mild-to-moderate CAN, who were aged 46 ± 11 years and had HbA1c 58 ± 5 mmol/mol (7.5 ± 1.0%), with no evidence of ischaemic heart disease. Participants underwent a 24-month intervention, consisting of antioxidant treatment with allopurinol, α-lipoic acid and nicotinamide, or placebo. The main outcome was change in the global [(11)C]HED retention index (RI) at 24 months in participants on the active drug compared with those on placebo.

RESULTS

We analysed data from 44 participants (22 per group). After adjusting for age, sex and in-trial HbA1c, the antioxidant regimen was associated with a slight, but significant worsening of the global [(11)C]HED left ventricle RI (-0.010 [95% CI -0.020, -0.001] p = 0.045) compared with placebo. There were no significant differences at follow-up between antioxidant treatment and placebo in the global MBF, coronary flow reserve, or in measures of DPN and markers of oxidative stress. The majority of adverse events were of mild-to-moderate severity and did not differ between groups

CONCLUSIONS/INTERPRETATION

In this cohort of type 1 diabetes patients with mild-to-moderate CAN, a combination antioxidant treatment regimen did not prevent progression of CAN, had no beneficial effects on myocardial perfusion or DPN, and may have been detrimental. However, a larger study is necessary to assess the underlying causes of these findings.

Inflammation and airway microbiota during cystic fibrosis pulmonary exacerbations

Background

Pulmonary exacerbations (PEx), frequently associated with airway infection and inflammation, are the leading cause of morbidity in cystic fibrosis (CF). Molecular microbiologic approaches detect complex microbiota from CF airway samples taken during PEx. The relationship between airway microbiota, inflammation, and lung function during CF PEx is not well understood.

Objective

To determine the relationships between airway microbiota, inflammation, and lung function in CF subjects treated for PEx.

Methods

Expectorated sputum and blood were collected and lung function testing performed in CF subjects during early (0–3d.) and late treatment (>7d.) for PEx. Sputum was analyzed by culture, pyrosequencing of 16S rRNA amplicons, and quantitative PCR for total and specific bacteria. Sputum IL-8 and neutrophil elastase (NE); and circulating C-reactive protein (CRP) were measured.

Results

Thirty-seven sputum samples were collected from 21 CF subjects. At early treatment, lower diversity was associated with high relative abundance (RA) of Pseudomonas (r = −0.67, p<0.001), decreased FEV_1% predicted (r = 0.49, p = 0.03) and increased CRP (r = −0.58, p = 0.01). In contrast to Pseudomonas, obligate and facultative anaerobic genera were associated with less inflammation and higher FEV₁. With treatment, Pseudomonas RA and P. aeruginosa by qPCR decreased while anaerobic genera showed marked variability in response. Change in RA of Prevotella was associated with more variability in FEV₁ response to treatment than Pseudomonas or Staphylococcus.

Conclusions

Anaerobes identified from sputum by sequencing are associated with less inflammation and higher lung function compared to Pseudomonas at early exacerbation. CF PEx treatment results in variable changes of anaerobic genera suggesting the need for larger studies particularly of patients without traditional CF pathogens.

Atomistic Simulations Predict a Surprising Variety of Morphologies in Precise Ionomers

The nature of ionic aggregates in ionomers remains an important open question, particularly considering its significance to their unique electrical and mechanical properties. We have carried out fully atomistic molecular dynamics simulations of melts of lithium-neutralized precise ionomers that reveal the structural features of ionic aggregates in unprecedented detail. In particular, we observe a rich variety of aggregate morphologies depending on neutralization level and ionic content, including string-like and percolated aggregates. The traditional assumption of spherical ionic aggregates with liquid-like ordering that is typically used to interpret experimental scattering data is too simplistic; a more rich and complex set of structures exist that also fit the scattering data.

Site-dipole field and vortices in confined water

We use molecular dynamics simulations to examine how the spatial patterns formed by the diffusive motion of water molecules are influenced by confinement between hydrophilic and hydrophobic surfaces. For bulk liquid water, Higo et al. found that the long-range orientational order of spatial dipole moments can form vortex-like spatial patterns for as long as 300 ps [Higo et al., Proc. Natl. Acad. Sci. USA 98, 5961 (2001)]. We perform a similar analysis for confined water and we find that the existence of vortices in these systems is dependent on both the surface separation and the surface hydrophilicity. Vortices perpendicular to the surface normal disappear when the surface separation is reduced to a thickness where the system is comprised of mostly interfacial water molecules. Vortices exist at slightly smaller separations for hydrophobic surfaces than for hydrophilic surfaces because the dipoles are less aligned at the hydrophobic surfaces. The dipole alignment that is induced by the hydrophilic surfaces is counter to the direction required by vortices.

Novel device to sample the esophageal microbiome--the esophageal string test

A growing number of studies implicate the microbiome in the pathogenesis of intestinal inflammation. Previous work has shown that adults with esophagitis related to gastroesophageal reflux disease have altered esophageal microbiota compared to those who do not have esophagitis. In these studies, sampling of the esophageal microbiome was accomplished by isolating DNA from esophageal biopsies obtained at the time of upper endoscopy. The aim of the current study was to identify the esophageal microbiome in pediatric individuals with normal esophageal mucosa using a minimally invasive, capsule-based string technology, the Enterotest™. We used the proximal segment of the Enterotest string to sample the esophagus, and term this the "Esophageal String Test" (EST). We hypothesized that the less invasive EST would capture mucosal adherent bacteria present in the esophagus in a similar fashion as mucosal biopsy. EST samples and mucosal biopsies were collected from children with no esophageal inflammation (n = 15) and their microbiome composition determined by 16S rRNA gene sequencing. Microbiota from esophageal biopsies and ESTs produced nearly identical profiles of bacterial genera and were different from the bacterial contents of samples collected from the nasal and oral cavity. We conclude that the minimally invasive EST can serve as a useful device for study of the esophageal microbiome.

Comparison of the kinetic friction of planar neutral and polyelectrolyte polymer brushes using molecular dynamics simulations

We have simulated the relative shear motion of both neutral and polyelectrolyte end-grafted polymer brushes using molecular dynamics. The flexible neutral polymer brush is treated as a bead-spring model, and the polyelectrolyte brush is treated the same way except that each bead is charged and there are counterions present to neutralize the charge. We investigated the friction coefficient, monomer density, and brush penetration for both polyelectrolyte and neutral brushes with both equal grafting density and equal normal force under good solvent conditions. We found that polyelectrolyte brushes had a smaller friction coefficient and monomer penetration than neutral polymer brushes with the identical grafting density and chain length, and the polyelectrolyte brushes supported a much higher normal load than the neutral brushes for the same degree of compression. Charged and neutral brushes with their grafting densities chosen so that they support the same load exhibited approximately the same degree of interpenetration, but the polyelectrolyte brush exhibited a significantly lower friction coefficient. We present evidence that the reason for this is that the extra normal force contribution provided by the counterion osmotic pressure that exists for polyelectrolyte brushes permits them to support the same load as an identical neutral polymer brush of higher grafting density. Because of the resulting lower monomer density for the charged brushes, fewer monomer collisions take place per unit time, resulting in a lower friction coefficient.

Ionic aggregate structure in ionomer melts: effect of molecular architecture on aggregates and the ionomer peak

We perform a comprehensive set of coarse-grained molecular dynamics simulations of ionomer melts with varying polymer architectures and compare the results to experiments in order to understand ionic aggregation on a molecular level. The model ionomers contain periodically or randomly spaced charged beads, placed either within or pendant to the polymer backbone, with the counterions treated explicitly. The ionic aggregate structure was determined as a function of the spacing of charged beads and also depends on whether the charged beads are in the polymer backbone or pendant to the backbone. The low wavevector ionomer peak in the counterion scattering is observed for all systems, and it is sharpest for ionomers with periodically spaced pendant charged beads with a large spacing between charged beads. Changing to a random or a shorter spacing moves the peak to lower wavevector. We present new experimental X-ray scattering data on Na(+)-neutralized poly(ethylene-co-acrylic acid) ionomers that show the same two trends in the ionomer peak, for similarly structured ionomers. The order within and between aggregates, and how this relates to various models used to fit the ionomer peak, is quantified and discussed.

Effect of polymer architecture and ionic aggregation on the scattering peak in model ionomers

We perform molecular dynamics simulations of coarse-grained ionomer melts with two different architectures. Regularly spaced charged beads are placed either in the polymer backbone (ionenes) or pendant to it. The ionic aggregate structure is quantified as a function of the dielectric constant. The low wave vector ionomer scattering peak is present in all cases, but is significantly more intense for pendant ions, which form compact, discrete aggregates with liquidlike interaggregate order. This is in qualitative contrast to the ionenes, which form extended aggregates.

Reliability of quantitative real-time PCR for bacterial detection in cystic fibrosis airway specimens

The cystic fibrosis (CF) airway microbiome is complex; polymicrobial infections are common, and the presence of fastidious bacteria including anaerobes make culture-based diagnosis challenging. Quantitative real-time PCR (qPCR) offers a culture-independent method for bacterial quantification that may improve diagnosis of CF airway infections; however, the reliability of qPCR applied to CF airway specimens is unknown. We sought to determine the reliability of nine specific bacterial qPCR assays (total bacteria, three typical CF pathogens, and five anaerobes) applied to CF airway specimens. Airway and salivary specimens from clinically stable pediatric CF subjects were collected. Quantitative PCR assay repeatability was determined using triplicate reactions. Split-sample measurements were performed to measure variability introduced by DNA extraction. Results from qPCR were compared to standard microbial culture for Pseudomonas aeruginosa, Staphylococcus aureus, and Haemophilus influenzae, common pathogens in CF. We obtained 84 sputa, 47 oropharyngeal and 27 salivary specimens from 16 pediatric subjects with CF. Quantitative PCR detected bacterial DNA in over 97% of specimens. All qPCR assays were highly reproducible at quantities ≥10² rRNA gene copies/reaction with coefficient of variation less than 20% for over 99% of samples. There was also excellent agreement between samples processed in duplicate. Anaerobic bacteria were highly prevalent and were detected in mean quantities similar to that of typical CF pathogens. Compared to a composite gold standard, qPCR and culture had variable sensitivities for detection of P. aeruginosa, S. aureus and H. influenzae from CF airway samples. By reliably quantifying fastidious airway bacteria, qPCR may improve our understanding of polymicrobial CF lung infections, progression of lung disease and ultimately improve antimicrobial treatments.

Conformational dynamics of neurofilament side-arms

The side-arms of neurofilaments (NFs) have been proposed to be highly disordered, leading to entropic repulsion that modulates interfilament spacing. To gain further insight into the dynamics and organization of the side-arms, we performed molecular dynamics simulations of neurofilament brushes using a coarse-grained model. The density profiles for three NF proteins, NF-L, NF-M, and phosphorylated NF-H (NF-HP), grafted to planar surfaces were calculated and examined as a function of component (salt, residues) and as a function of charge. Analysis of these profiles reveals that the NF with the shortest side arm, NF-L, is disproportionately long compared to the other NFs. The reason for difference is that NF-L is effectively a strong polyelectrolyte, while NF-M and NF-HP are effectively weaker polyelectrolytes. Further, we find cross-correlations between neurofilament side-arms within the brush, even for the NF-L polymers. These correlations occur because of strong attractions between the long sequence repeats of negative residues and the long postive residue repeats and impart a time average structure of the neurofilament brush that deviates from an ideal polymer in a theta solvent.

Splaying of aliphatic tails plays a central role in barrier crossing during liposome fusion

The fusion between two lipid bilayers involves crossing a complicated energy landscape. The limiting barrier in the process appears to be between two closely opposed bilayers and the intermediate state where the outer leaflets are fused. We have performed molecular dynamics simulations to characterize the free energy barrier for the fusion of two liposomes and to examine the molecular details of barrier crossing. To capture the slow dynamics of fusion, a model using coarse-grained representations of lipids was used. The fusion between pairs of liposomes was simulated for four systems: DPPC, DOPC, a 3:1 mixture of DPPC/DPPE, and an asymmetric lipid tail system in which one tail of DPPC was reduced to half the length (ASTail). The weighted histogram method was used to compute the free energy as a function of separation distance. The relative barrier heights for these systems was found to be ASTail >> DPPC > DPPC/DPPE > DOPC, in agreement with experimental observations. Further, the free energy curves for all four can be overlaid on a single curve by plotting the free energy versus the surface separation (differing only in the point of fusion). These simulations also confirm that the two main contributions to the free energy barrier are the removal of water between the vesicles and the deformation of the vesicle. The most prominent molecular detail of barrier crossing in all cases examined was the splaying of lipid tails, where initially a single splayed lipid formed a bridge between the two outer leaflets that promotes additional lipid mixing between the vesicles and eventually leads to fusion. The tail splay appears to be closely connected to the energetics of the process. For example, the high barrier for the ASTail is the result of a smaller distance between terminal methyl groups in the splayed molecule. The shortening of this distance requires the liposomes to be closer together, which significantly increases the cost of water removal and bilayer deformation. Before tail splay can initiate fusion, contact must occur between a tail end and the external water. In isolated vesicles, the contact fraction is correlated to the fusogenicity difference between DPPC and DOPC. Moreover, for planar bilayers, the contact fraction is much lower for DPPC, which is consistent with its lack of fusion in giant vesicles. The simulation results show the key roles of lipid tail dynamics in governing the fusion energy landscape.

Examining the origins of the hydration force between lipid bilayers using all-atom simulations

Using 237 all-atom double bilayer simulations, we examined the thermodynamic and structural changes that occur as a phosphatidylcholine lipid bilayer stack is dehydrated. The simulated system represents a micropatch of lipid multilayer systems that are studied experimentally using surface force apparatus, atomic force microscopy and osmotic pressure studies. In these experiments, the hydration level of the system is varied, changing the separation between the bilayers, in order to understand the forces that the bilayers feel as they are brought together. These studies have found a curious, strongly repulsive force when the bilayers are very close to each other, which has been termed the "hydration force," though the origins of this force are not clearly understood. We computationally reproduce this repulsive, relatively free energy change as bilayers come together and make qualitative conclusions as to the enthalpic and entropic origins of the free energy change. This analysis is supported by data showing structural changes in the waters, lipids and salts that have also been seen in experimental work. Increases in solvent ordering as the bilayers are dehydrated are found to be essential in causing the repulsion as the bilayers come together.

Oxide-dependent adhesion of the Jurkat line of T lymphocytes

The adhesion force of Jurkat cells was measured using atomic force microscopy (AFM) in aqueous solution at pH 7.2 on six metal oxide surfaces, namely, two quartz (alpha-SiO2) crystal faces, amorphous SiO2 glass, rutile (alpha-TiO2), muscovite mica (KAl2(AlSi3O10)(OH)2), and polycrystalline corundum (alpha-Al2O3). We show quantitatively for the first time that the T lymphocyte adhesion force and adhesion work correlates with substrate point of zero charge, indicating greater adsorption on surfaces with smaller negative charge. Adhesion events also exhibited sawtooth-shaped force-distance profiles indicative of protein bonds. No significant correlations were found with oxide Hamaker constants, indicating negligible contributions from van der Waals forces, nor with surface roughness. These results suggest that, when cell-surface receptors are not activated, Jurkat cell adhesion is dominated by specific interactions related to the unfolding of modular glycoproteins or other proteins that are not unique to T-cell surfaces and by electrostatic forces between negatively charged glycoproteins and variably charged oxide surfaces. Our results have implications for the interactions of immune system cells with metal oxides present in the human body either by design as in biomedical applications or inadvertently such as inhaled mineral dust particles in the lung.