1
|
Frischknecht AL, Stevens MJ. Force Fields for High Concentration Aqueous KOH Solutions and Zincate Ions. J Phys Chem B 2024; 128:3475-3484. [PMID: 38547112 DOI: 10.1021/acs.jpcb.3c08302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Motivated by increasing interest in electrochemical devices that include highly alkaline electrolytes, we investigated two force fields for potassium hydroxide (KOH) at high concentrations in water. The "FNB" model uses the SPC/E water model, while the "FHM" model uses the TIP4P/2005 water model. We also developed parameters to describe zincate ions in these solutions. The density and viscosity of KOH using the FHM model are in better agreement with experiment than the values from the FNB model. Comparing the properties of the zincate solutions to the available experimental data, we find that both force fields agree reasonably well, although the FHM parameters give a better prediction of the viscosity. The developed force field parameters can be used in future simulations of zincate/KOH solutions in combination with other species of interest.
Collapse
Affiliation(s)
- Amalie L Frischknecht
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| |
Collapse
|
2
|
Stevens MJ, Rempe SLB. Insight into the K channel's selectivity from binding of K +, Na + and water to N-methylacetamide. Faraday Discuss 2024; 249:195-209. [PMID: 37846738 DOI: 10.1039/d3fd00110e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
In potassium channels that conduct K+ selectively over Na+, which sites are occupied by K+ or water and the mechanism of selectivity are unresolved questions. The combination of the energetics and the constraints imposed by the protein structure yield the selective permeation and occupancy. To gain insight into the combination of structure and energetics, we performed density functional theory (DFT) calculations of multiple N-methyl acetamide (NMA) ligands binding to K+ and Na+, relative to hydrated K+ and Na+. NMA is an analogue of the amino acid backbone and provides the carbonyl binding to the ions that occurs in most binding sites of the K+ channel. Unconstrained optimal structures are obtained through geometry optimization calculations of the NMA ligand binding. The complexes formed by 8 NMA binding to the cations have the O atoms positioned in nearly identical locations as the O atoms in the selectivity filter. The transfer free energies between bulk water and K+ or Na+ bound to 8 NMA are almost identical, implying there is no selectivity by a single site. For water optimized with 8 NMA, binding is weak and O atoms are not positioned as in the K+ channel selectivity filter, suggesting that the ions are much more favored than water. Optimal structures of 8 NMA binding with two cations (K+ or Na+) are stable and have lower binding free energy than the optimal structures with just one cation. However, in the Na+ case, the optimal structure deforms and does not match the K+ channel; that is, two bound Na+ are destabilizing. In contrast, the two K+ structure is stabilized and the selectivity free energy favors K+. Overall, this study shows that binding site occupancy and the mechanism for K+ selectivity involves multiple K+ binding in multiple neighboring layers or sites of the K+ channel selectivity filter.
Collapse
Affiliation(s)
- Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
| | - Susan L B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
| |
Collapse
|
3
|
Stevens MJ, Rempe SLB. Binding of Li + to Negatively Charged and Neutral Ligands in Polymer Electrolytes. J Phys Chem Lett 2023; 14:10200-10207. [PMID: 37930189 DOI: 10.1021/acs.jpclett.3c02565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Conceptually, single-ion polymer electrolytes (SIPE) with the anion bound to the polymer could solve major issues in Li-ion batteries, but their conductivity is too low. Experimentally, weakly interacting anionic groups have the best conductivity. To provide a theoretical basis for this result, density functional theory calculations of the optimized geometries and energies are performed for charged ligands used in SIPE. Comparison is made to neutral ligands found in dual-ion conductors, which demonstrate higher conductivity. The free energy differences between adding and subtracting a ligand are small enough for the neutral ligands to have the conductivity seen experimentally. However, charged ligands have large barriers, implying that lithium transport will coincide with the slow polymer diffusion, as observed in experiments. Overall, SIPE will require additional solvent to achieve a sufficiently high conductivity. Additionally, the binding of mono- and bidentate geometries varies, providing a simple and clear reason that polarizable force fields are required for detailed interactions.
Collapse
Affiliation(s)
- Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Susan L B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| |
Collapse
|
4
|
Stevens MJ, Rempe SLB. Binding of carboxylate and water to monovalent cations. Phys Chem Chem Phys 2023; 25:29881-29893. [PMID: 37889481 DOI: 10.1039/d3cp04200f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The interactions of carboxylate anions with water and cations are important for a wide variety of systems, both biological and synthetic. To gain insight on properties of the local complexes, we apply density functional theory, to treat the complex electrostatic interactions, and investigate mixtures with varied numbers of carboxylate anions (acetate) and waters binding to monovalent cations, Li+, Na+ and K+. The optimal structure with overall lowest free energy contains two acetates and two waters such that the cation is four-fold coordinated, similar to structures found earlier for pure water or pure carboxylate ligands. More generally, the complexes with two acetates have the lowest free energy. In transitioning from the overall optimal state, exchanging an acetate for water has a lower free energy barrier than exchanging water for an acetate. In most cases, the carboxylates are monodentate and in the first solvation shell. As water is added to the system, hydrogen bonding between waters and carboxylate O atoms further stabilizes monodentate structures. These structures, which have strong electrostatic interactions that involve hydrogen bonds of varying strength, are significantly polarized, with ChelpG partial charges that vary substantially as the bonding geometry varies. Overall, these results emphasize the increasing importance of water as a component of binding sites as the number of ligands increases, thus affecting the preferential solvation of specific metal ions and clarifying Hofmeister effects. Finally, structural analysis correlated with free energy analysis supports the idea that binding to more than the preferred number of carboxylates under architectural constraints are a key to ion transport.
Collapse
Affiliation(s)
- Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
| | - Susan L B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
| |
Collapse
|
5
|
Wagner BD, Zemanick ET, Sagel SD, Robertson CE, Stevens MJ, Mayer-Hamblett N, Retsch-Bogart G, Ramsey BW, Harris JK. Limited effects of azithromycin on the oropharyngeal microbiome in children with CF and early pseudomonas infection. BMC Microbiol 2023; 23:312. [PMID: 37891457 PMCID: PMC10612347 DOI: 10.1186/s12866-023-03073-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Tobramycin inhalation solution (TIS) and chronic azithromycin (AZ) have known clinical benefits for children with CF, likely due to antimicrobial and anti-inflammatory activity. The effects of chronic AZ in combination with TIS on the airway microbiome have not been extensively investigated. Oropharyngeal swab samples were collected in the OPTIMIZE multicenter, randomized, placebo-controlled trial examining the addition of AZ to TIS in 198 children with CF and early P. aeruginosa infection. Bacterial small subunit rRNA gene community profiles were determined. The effects of TIS and AZ were assessed on oropharyngeal microbial diversity and composition to uncover whether effects on the bacterial community may be a mechanism of action related to the observed changes in clinical outcomes. RESULTS Substantial changes in bacterial communities (total bacterial load, diversity and relative abundance of specific taxa) were observed by week 3 of TIS treatment for both the AZ and placebo groups. On average, these shifts were due to changes in non-traditional CF taxa that were not sustained at the later study visits (weeks 13 and 26). Bacterial community measures did not differ between the AZ and placebo groups. CONCLUSIONS This study provides further evidence that the mechanism for AZ's effect on clinical outcomes is not due solely to action on airway microbial composition.
Collapse
Affiliation(s)
- Brandie D Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, USA.
- Children's Hospital Colorado, Aurora, CO, USA.
| | - Edith T Zemanick
- Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | - Scott D Sagel
- Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | | | - Mark J Stevens
- Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | - Nicole Mayer-Hamblett
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Seattle Children's Hospital, Seattle, WA, USA
| | | | - Bonnie W Ramsey
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Seattle Children's Hospital, Seattle, WA, USA
| | - J Kirk Harris
- Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado, Aurora, CO, USA
| |
Collapse
|
6
|
Taylor PA, Stevens MJ. Explicit solvent machine-learned coarse-grained model of sodium polystyrene sulfonate to capture polymer structure and dynamics. Eur Phys J E Soft Matter 2023; 46:97. [PMID: 37831216 DOI: 10.1140/epje/s10189-023-00355-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023]
Abstract
Strongly charged polyelectrolytes (PEs) demonstrate complex solution behavior as a function of chain length, concentrations, and ionic strength. The viscosity behavior is important to understand and is a core quantity for many applications, but aspects remain a challenge. Molecular dynamics simulations using implicit solvent coarse-grained (CG) models successfully reproduce structure, but are often inappropriate for calculating viscosities. To address the need for CG models which reproduce viscoelastic properties of one of the most studied PEs, sodium polystyrene sulfonate (NaPSS), we report our recent efforts in using Bayesian optimization to develop CG models of NaPSS which capture both polymer structure and dynamics in aqueous solutions with explicit solvent. We demonstrate that our explicit solvent CG NaPSS model with the ML-BOP water model [Chan et al. Nat Commun 10, 379 (2019)] quantitatively reproduces NaPSS chain statistics and solution structure. The new explicit solvent CG model is benchmarked against diffusivities from atomistic simulations and experimental specific viscosities for short chains. We also show that our Bayesian-optimized CG model is transferable to larger chain lengths across a range of concentrations. Overall, this work provides a machine-learned model to probe the structural, dynamic, and rheological properties of polyelectrolytes such as NaPSS and aids in the design of novel, strongly charged polymers with tunable structural and viscoelastic properties.
Collapse
Affiliation(s)
- Phillip A Taylor
- Sandia National Laboratories, Center for Integrated Nanotechnologies, Albuquerque, NM, 87123, USA
| | - Mark J Stevens
- Sandia National Laboratories, Center for Integrated Nanotechnologies, Albuquerque, NM, 87123, USA.
| |
Collapse
|
7
|
Shock CJ, Stevens MJ, Frischknecht AL, Nakamura I. Molecular dynamics simulations of the dielectric constants of salt-free and salt-doped polar solvents. J Chem Phys 2023; 159:134507. [PMID: 37795785 DOI: 10.1063/5.0165481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/15/2023] [Indexed: 10/06/2023] Open
Abstract
We develop a Stockmayer fluid model that accounts for the dielectric responses of polar solvents (water, MeOH, EtOH, acetone, 1-propanol, DMSO, and DMF) and NaCl solutions. These solvent molecules are represented by Lennard-Jones (LJ) spheres with permanent dipole moments and the ions by charged LJ spheres. The simulated dielectric constants of these liquids are comparable to experimental values, including the substantial decrease in the dielectric constant of water upon the addition of NaCl. Moreover, the simulations predict an increase in the dielectric constant when considering the influence of ion translations in addition to the orientation of permanent dipoles.
Collapse
Affiliation(s)
- Cameron J Shock
- Department of Physics, Michigan Technological University, Houghton, Michigan 49931, USA
| | - Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Amalie L Frischknecht
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Issei Nakamura
- Department of Physics, Michigan Technological University, Houghton, Michigan 49931, USA
| |
Collapse
|
8
|
Vigil DL, Stevens MJ, Frischknecht AL. Accurate Calculation of Solvation Properties of Lithium Ions in Nonaqueous Solutions. J Phys Chem B 2023; 127:8002-8008. [PMID: 37676921 DOI: 10.1021/acs.jpcb.3c05591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
We perform all-atom molecular dynamics simulations of lithium triflate in 1,2-dimethoxyethane using six different literature force fields. This system is representative of many experimental studies of lithium salts in solvents and polymers. We show that multiple historically common force fields for lithium ions give qualitatively incorrect results when compared with those from experiments and quantum chemistry calculations. We illustrate the importance of correctly selecting force field parameters and give recommendations on the force field choice for lithium electrolyte applications.
Collapse
Affiliation(s)
- Daniel L Vigil
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Amalie L Frischknecht
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| |
Collapse
|
9
|
Harris JK, Wagner BD, Robertson CE, Stevens MJ, Lingard C, Borowitz D, Leung DH, Heltshe SL, Ramsey BW, Zemanick ET. Upper airway microbiota development in infants with cystic fibrosis diagnosed by newborn screen. J Cyst Fibros 2023; 22:644-651. [PMID: 37137746 PMCID: PMC10524365 DOI: 10.1016/j.jcf.2023.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/03/2023] [Accepted: 04/21/2023] [Indexed: 05/05/2023]
Abstract
BACKGROUND Changes in upper airway microbiota may impact early disease manifestations in infants with cystic fibrosis (CF). To investigate early airway microbiota, the microbiota present in the oropharynx of CF infants over the first year of life was assessed along with the relationships between microbiota and growth, antibiotic use and other clinical variables. METHODS Oropharyngeal (OP) swabs were collected longitudinally between 1 and 12 months of age from infants diagnosed with CF by newborn screen and enrolled in the Baby Observational and Nutrition Study (BONUS). DNA extraction was performed after enzymatic digestion of OP swabs. Total bacterial load was determined by qPCR and community composition assessed using 16S rRNA gene analysis (V1/V2 region). Changes in diversity with age were evaluated using mixed models with cubic B-splines. Associations between clinical variables and bacterial taxa were determined using a canonical correlation analysis. RESULTS 1,052 OP swabs collected from 205 infants with CF were analyzed. Most infants (77%) received at least one course of antibiotics during the study and 131 OP swabs were collected while the infant was prescribed an antibiotic. Alpha diversity increased with age and was only marginally impacted by antibiotic use. Community composition was most highly correlated with age and was only moderately correlated with antibiotic exposure, feeding method and weight z-scores. Relative abundance of Streptococcus decreased while Neisseria and other taxa increased over the first year. CONCLUSIONS Age was more influential on the oropharyngeal microbiota of infants with CF than clinical variables including antibiotics in the first year of life.
Collapse
Affiliation(s)
- J Kirk Harris
- Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, 13123 E. 16th Ave, B-395, Aurora, CO 80045, USA.
| | - Brandie D Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Charles E Robertson
- Department of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Mark J Stevens
- Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, 13123 E. 16th Ave, B-395, Aurora, CO 80045, USA
| | - Conor Lingard
- Spartanburg Regional Healthcare Systems, Spartanburg, SC, USA
| | - Drucy Borowitz
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | - Daniel H Leung
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Sonya L Heltshe
- Cystic Fibrosis Foundation Therapeutic Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, WA, USA; Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Bonnie W Ramsey
- Cystic Fibrosis Foundation Therapeutic Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, WA, USA; Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Edith T Zemanick
- Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, 13123 E. 16th Ave, B-395, Aurora, CO 80045, USA
| |
Collapse
|
10
|
Stevens MJ, Ko F, Martland J, Brown R, Bell L, Atyeo J, Yim J. Safety and efficacy of single insertion accelerated MR-image guided brachytherapy following chemo-radiation in locally advanced cervix cancer: modifying our EMBRACE during the COVID pandemic. Radiat Oncol 2023; 18:54. [PMID: 36941643 PMCID: PMC10026240 DOI: 10.1186/s13014-023-02240-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 03/06/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Utero-vaginal brachytherapy (BT) is an irreplaceable care component for the curative treatment of locally advanced cervix cancer (LACC). Magnetic Resonance Imaging (MRI)-image guided adaptive BT (IGABT) using the GYN-GEC-ESTRO EMBRACE guidelines is the international care standard. Usually following chemo-radiation therapy (CRT), IGABT has high proven utility in LACC but requires significant health system resources. Timely access was disrupted by the COVID-19 pandemic which challenged us to re-design our established IGABT care pathway. METHODS From April 2020 consecutive patients with LACC were enrolled after CRT in a single arm exploratory non-inferiority study of a modified IGABT (mIGABT) protocol. This delivered an iso-effective IGABT dose (39.3 Gy: EQD2: α/β10Gy concept) over a 24-h period during a single overnight hospitalisation. RESULTS Fourteen LACC patients received mIGABT from April 2020 to March 2022. Median age was 62.5 years (37-82 years). LACC histology was primary squamous (9/14) or adeno-carcinoma (5/14). International Federation of Gynaecology and Obstetrics (FIGO) 2018 stages ranged from IB1/2 (N = 3), IIA1/IIB (5), IIIB (2), IIIC1/2 (4) with mean ± standard deviation (SD) gross tumour volume-at-diagnosis (GTV_D) of 37.7 cc ± 71.6 cc. All patients achieved complete metabolic, clinical, and cytologic cancer response with CRT and IGABT. High-risk HPV was cleared by 6-months. Complete MRI-defined cancer response before mIGABT (GTV_Fx1) was seen in 77% of cases (10/13). Only two women developed metastatic disease and one died at 12-months; 13 patients were alive without cancer at mean 20.3 ± 7.2 months follow-up. Actuarial 2-year overall survival was 93%. Compared with our pre-COVID IGABT program, overall mIGABT cost-saving in this cohort was USD 22,866. Prescribed dose covered at least 90% (D90) of the entire cervix and any residual cancer at time of BT (HRCTV_D90: high-risk clinical target volume) with 3-fractions of 8.5 Gy delivered over 24-h (22.8 ± 1.7 h). Total treatment time including CRT was 38 days. The mIGABT schedule was well tolerated and the entire cohort met EMBRACE recommended (EQD2: α/β10Gy) combined HRCTV_D90 coverage of 87.5 ± 3.7 Gy. Similarly, organ-at-risk (OAR) median: interquartile range D2cc constraints (EQD2: α/β3Gy) were EMBRACE compliant: bladder (65.9 Gy: 58.4-72.5 Gy), rectum (59.1 Gy: 55.7-61.8 Gy), and sigmoid colon (54.6 Gy: 50.3-58.9 Gy). ICRU recto-vaginal point dose was significantly higher (75.7 Gy) in our only case of severe (G4) pelvic toxicity. CONCLUSIONS This study demonstrated the utility of mIGABT and VMAT CRT in a small cohort with LACC. Loco-regional control was achieved in all cases with minimal emergent toxicity. Single insertion mIGABT was logistically efficient, cost-saving, and patient-centric during the COVID-19 pandemic.
Collapse
Affiliation(s)
- Mark J Stevens
- Department of Radiation Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Level 1 ASB Building, St Leonards, NSW, 2065, Australia.
- Northern Clinical School, University of Sydney, St Leonards, NSW, Australia.
| | - Florence Ko
- Department of Radiation Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Level 1 ASB Building, St Leonards, NSW, 2065, Australia
| | - Judith Martland
- Department of Radiation Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Level 1 ASB Building, St Leonards, NSW, 2065, Australia
| | - Ryan Brown
- Department of Radiation Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Level 1 ASB Building, St Leonards, NSW, 2065, Australia
| | - Linda Bell
- Department of Radiation Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Level 1 ASB Building, St Leonards, NSW, 2065, Australia
| | - John Atyeo
- Department of Radiation Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Level 1 ASB Building, St Leonards, NSW, 2065, Australia
| | - Jackie Yim
- Department of Radiation Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Level 1 ASB Building, St Leonards, NSW, 2065, Australia
| |
Collapse
|
11
|
Furuta GT, Fillon SA, Williamson KM, Robertson CE, Stevens MJ, Aceves SS, Arva NC, Chehade M, Collins MH, Davis CM, Dellon ES, Falk GW, Gonsalves N, Gupta SK, Hirano I, Khoury P, Leung J, Martin LJ, Menard-Katcher P, Mukkada VA, Peterson K, Spergel JM, Wechsler JB, Yang GY, Rothenberg ME, Harris JK. Mucosal Microbiota Associated With Eosinophilic Esophagitis and Eosinophilic Gastritis. J Pediatr Gastroenterol Nutr 2023; 76:347-354. [PMID: 36525669 PMCID: PMC10201396 DOI: 10.1097/mpg.0000000000003685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
OBJECTIVE The aim of the study was to determine the mucosal microbiota associated with eosinophilic esophagitis (EoE) and eosinophilic gastritis (EoG) in a geographically diverse cohort of patients compared to controls. METHODS We conducted a prospective study of individuals with eosinophilic gastrointestinal disease (EGID) in the Consortium of Eosinophilic Gastrointestinal Disease Researchers, including pediatric and adult tertiary care centers. Eligible individuals had clinical data, mucosal biopsies, and stool collected. Total bacterial load was determined from mucosal biopsy samples by quantitative polymerase chain reaction (PCR). Community composition was determined by small subunit rRNA gene amplicons. RESULTS One hundred thirty-nine mucosal biopsies were evaluated corresponding to 93 EoE, 17 EoG, and 29 control specimens (18 esophageal) from 10 sites across the United States. Dominant community members across disease activity differed significantly. When comparing EoE and EoG with controls, the dominant taxa in individuals with EGIDs was increased ( Streptococcus in esophagus; Prevotella in stomach). Specific taxa were associated with active disease for both EoE ( Streptococcus , Gemella ) and EoG ( Leptotrichia ), although highly individualized communities likely impacted statistical testing. Alpha diversity metrics were similar across groups, but with high variability among individuals. Stool analyses did not correlate with bacterial communities found in mucosal biopsy samples and was similar in patients and controls. CONCLUSIONS Dominant community members ( Streptococcus for EoE, Prevotella for EoG) were different in the mucosal biopsies but not stool of individuals with EGIDs compared to controls; taxa associated with EGIDs were highly variable across individuals. Further study is needed to determine if therapeutic interventions contribute to the observed community differences.
Collapse
Affiliation(s)
- Glenn T. Furuta
- Section of Pediatric Gastroenterology, Hepatology and Nutrition, Digestive Health Institute, Children’s Hospital Colorado, Gastrointestinal Eosinophilic Disease Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO
| | - Sophie A. Fillon
- Section of Pediatric Gastroenterology, Hepatology and Nutrition, Digestive Health Institute, Children’s Hospital Colorado, Gastrointestinal Eosinophilic Disease Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO
| | - Kayla M. Williamson
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado School of Medicine, Aurora, CO
| | - Charles E. Robertson
- Division of Infectious Disease, University of Colorado School of Medicine, Aurora, CO
| | - Mark J. Stevens
- Division of Infectious Disease, University of Colorado School of Medicine, Aurora, CO
| | - Seema S. Aceves
- Division of Allergy/Immunology, Department of Pediatrics, University of California, San Diego, Rady Children’s Hospital, San Diego, CA
| | - Nicoleta C. Arva
- Department of Pathology, Ann & Robert H Lurie Children’s Hospital of Chicago, Chicago, IL
| | - Mirna Chehade
- Departments of Pediatrics and Medicine, Mount Sinai Center for Eosinophilic Disorders, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Margaret H. Collins
- Division of Pathology and Laboratory Medicine, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati, Cincinnati, OH
| | - Carla M. Davis
- Division of Immunology, Allergy and Retrovirology, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX
| | - Evan S. Dellon
- Center for Esophageal Diseases and Swallowing and Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Gary W. Falk
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Nirmala Gonsalves
- Division of Gastroenterology and Hepatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Sandeep K. Gupta
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Riley Hospital for Children/Indiana University School of Medicine, and Community Health Network, Indianapolis, IN
| | - Ikuo Hirano
- Division of Gastroenterology and Hepatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Paneez Khoury
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Human Eosinophil Section, NIAID, Bethesda, MD
| | - John Leung
- Divisions of Allergy/Immunology and Gastroenterology, Tuft’s Medical Center, Boston, MA
| | - Lisa J. Martin
- Department of Pediatrics, Cincinnati Children’s Hospital and the University of Cincinnati College of Medicine, Cincinnati, OH
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati, Cincinnati, OH
| | | | - Vincent A. Mukkada
- Division of Gastroenterology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati, Cincinnati, OH
| | - Kathryn Peterson
- Division of Gastroenterology, University of Utah, Salt Lake City, UT
| | - Jonathan M. Spergel
- Division of Allergy and Immunology, Children’s Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine of University of Pennsylvania, Philadelphia, PA
| | - Joshua B. Wechsler
- Division of Gastroenterology, Hepatology, and Nutrition, Ann & Robert H Lurie Children’s Hospital of Chicago, Chicago, IL
| | - Guang-Yu Yang
- Division of Gastrointestinal Pathology, Department of Pathology, Fineberg School of Medicine, Northwestern University, Chicago, IL
| | - Marc E. Rothenberg
- Division of Allergy/Immunology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH
| | - J. Kirk Harris
- Breathing Institute, Section of Pediatric Pulmonology, Children’s Hospital Colorado, University of Colorado School of Medicine, Aurora, CO
| |
Collapse
|
12
|
Hall DM, Stevens MJ, Grason GM. Building blocks of non-Euclidean ribbons: size-controlled self-assembly via discrete frustrated particles. Soft Matter 2023; 19:858-881. [PMID: 36636841 DOI: 10.1039/d2sm01371a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Geometric frustration offers a pathway to soft matter self-assembly with controllable finite sizes. While the understanding of frustration in soft matter assembly derives almost exclusively from continuum elastic descriptions, a current challenge is to understand the connection between microscopic physical properties of misfitting "building blocks" and emergent assembly behavior at the mesoscale. We present and analyze a particle-based description of what is arguably the best studied example for frustrated soft matter assembly, negative-curvature ribbon assembly, observed in both assemblies of chiral surfactants and shape-frustrated nanoparticles. Based on our particle model, known as saddle wedge monomers, we numerically test the connection between microscopic shape and interactions of the misfitting subunits and the emergent behavior at the supra-particle scale, specifically focussing on the propagation and relaxation of inter-particle strains, the emergent role of extrinsic shape on frustrated ribbons and the equilibrium regime of finite width selection. Beyond the intuitive role of shape misfit, we show that self-limitation is critically dependent on the finite range of cohesive interactions, with larger size finite assemblies requiring increasing short-range interparticle forces. Additionally, we demonstrate that non-linearities arising from discrete particle interactions alter self-limiting behavior due to both strain-softening in shape-flattened assembly and partial yielding of highly strained bonds, which in turn may give rise to states of hierarchical, multidomain assembly. Tracing the regimes of frustration-limited assembly to the specific microscopic features of misfitting particle shapes and interactions provides necessary guidance for translating the theory of size-programmable assembly into design of intentionally-frustrated colloidal particles.
Collapse
Affiliation(s)
- Douglas M Hall
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA.
| | - Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA
| | - Gregory M Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA.
| |
Collapse
|
13
|
Walker-Bone K, D’Angelo S, Linaker CH, Stevens MJ, Ntani G, Cooper C, Syddall HE. Morbidities among older workers and work exit: the HEAF cohort. Occup Med (Lond) 2022; 72:470-477. [PMID: 35904117 PMCID: PMC9578672 DOI: 10.1093/occmed/kqac068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Governments need people to work to older ages, but the prevalence of chronic disease and comorbidity increases with age and impacts work ability. AIMS To investigate the effects of objective health diagnoses on exit from paid work amongst older workers. METHODS Health and Employment After Fifty (HEAF) is a population cohort of adults aged 50-64 years recruited from English GP practices which contribute to the Clinical Practice Research Datalink (CPRD). Participants have completed questionnaires about health and work at baseline and annually for 2 years: their responses were linked with their objective health diagnoses from the CPRD and data analysed using Cox regression. RESULTS Of 4888 HEAF participants ever in paid work, 580 (25%) men and 642 (25%) women exited employment, 277 of them mainly or partly for a health reason (health-related job loss (HRJL)). Amongst HEAF participants who remained in work (n = 3666) or who exited work but not for health reasons (n = 945), there was a similar prevalence of background health conditions. In men and women, HRJL was associated with inflammatory arthritis, sleep disorders, common mental health conditions and musculoskeletal pain. There were however gender differences: widespread pain and lower limb osteoarthritis were associated with HRJL in women but hypertension and cardiovascular disease in men. CONCLUSIONS Improved diagnosis and management of common conditions might be expected to increase working lives. Workplace well-being interventions targeting obesity and increasing mobility might contribute to extended working lives. Employers of predominantly female, as compared with male workforces may need different strategies to retain older workers.
Collapse
Affiliation(s)
- K Walker-Bone
- MRC Versus Arthritis Centre for Musculoskeletal Health and Work, University of Southampton SO16 6YD, Southampton, UK
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton SO16 6YD, UK
- Monash Centre for Occupational and Environmental Health, Monash University, Melbourne, Australia
| | - S D’Angelo
- MRC Versus Arthritis Centre for Musculoskeletal Health and Work, University of Southampton SO16 6YD, Southampton, UK
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton SO16 6YD, UK
| | - C H Linaker
- MRC Versus Arthritis Centre for Musculoskeletal Health and Work, University of Southampton SO16 6YD, Southampton, UK
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton SO16 6YD, UK
| | - M J Stevens
- MRC Versus Arthritis Centre for Musculoskeletal Health and Work, University of Southampton SO16 6YD, Southampton, UK
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton SO16 6YD, UK
| | - G Ntani
- MRC Versus Arthritis Centre for Musculoskeletal Health and Work, University of Southampton SO16 6YD, Southampton, UK
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton SO16 6YD, UK
| | - C Cooper
- MRC Versus Arthritis Centre for Musculoskeletal Health and Work, University of Southampton SO16 6YD, Southampton, UK
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton SO16 6YD, UK
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
- National Institute for Health Research Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - H E Syddall
- MRC Versus Arthritis Centre for Musculoskeletal Health and Work, University of Southampton SO16 6YD, Southampton, UK
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton SO16 6YD, UK
| |
Collapse
|
14
|
Stevens MJ, Rempe SLB. Carboxylate binding prefers two cations to one. Phys Chem Chem Phys 2022; 24:22198-22205. [PMID: 36093927 DOI: 10.1039/d2cp03561h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Almost all studies of specific ion binding by carboxylates (-COO-) have considered only a single cation, but clustering of ions and ligands is a common phenomenon. We apply density functional theory to investigate how variations in the number of acetate ligands in binding to two monovalent cations affects ion binding preferences. We study a series of monovalent (Li+, Na+, K+, Cs+) ions relevant to experimental work on many topics, including ion channels, battery storage, water purification and solar cells. We find that the preferred optimal structure has 3 acetates except for Cs+, which has 2 acetates. The optimal coordination of the cation by the carboxylate O atoms is 4 for both Na+ and K+, and 3 for Li+ and Cs+. There is a 4-fold coordination minimum just a few kcal mol-1 higher than the optimal 3-fold structure for Li+. For two cations, multiple minima occur in the vicinity of the lowest free energy state. We find that, for Li, Na and K, the preferred optimal structure with two cations is favored over a mixture of single cation complexes, providing a basis for understanding ionic cluster formation that is relevant for engineering proteins and other materials for rapid, selective ion transport.
Collapse
Affiliation(s)
- Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
| | - Susan L B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA. .,CBRN Defense and Energy Technologies, Sandia National Laboratories, Albuquerque, NM, 87185, USA.
| |
Collapse
|
15
|
Abstract
BACKGROUND UK Biobank (UKB) is a large prospective cohort capturing numerous health outcomes, but limited occupational information (job title, self-reported manual work and occupational walking/standing). AIMS To create and evaluate validity of a linkage between UKB and a job exposure matrix for physical work exposures based on the US Occupational Information Network (O*NET) database. METHODS Job titles and UK Standard Occupational Classification (SOC) codes were collected during UKB baseline assessment visits. Using existing crosswalks, UK SOC codes were mapped to US SOC codes allowing linkage to O*NET variables capturing numerous dimensions of physical work. Job titles with the highest O*NET scores were assessed to evaluate face validity. Spearman's correlation coefficients were calculated to compare O*NET scores to self-reported UKB measures. RESULTS Among 324 114 participants reporting job titles, 323 936 were linked to O*NET. Expected relationships between scores and self-reported measures were observed. For static strength (0-7 scale), the median O*NET score was 1.0 (e.g. audiologists), with a highest score of 4.88 for stone masons and a positive correlation with self-reported heavy manual work (Spearman's coefficient = 0.50). For time spent standing (1-5 scale), the median O*NET score was 2.72 with a highest score of 5 for cooks and a positive correlation with self-reported occupational walking/standing (Spearman's coefficient = 0.56). CONCLUSIONS While most jobs were not physically demanding, a wide range of physical work values were assigned to a diverse set of jobs. This novel linkage of a job exposure matrix to UKB provides a potentially valuable tool for understanding relationships between occupational exposures and disease.
Collapse
Affiliation(s)
- E L Yanik
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Department of Surgery, Washington University School of Medicine, St.Louis, MO, USA
| | - M J Stevens
- MRC Versus Arthritis Centre for Musculoskeletal Health and Work, University of Southampton, Southampton, UK
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
| | - E Clare Harris
- MRC Versus Arthritis Centre for Musculoskeletal Health and Work, University of Southampton, Southampton, UK
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
| | - K E Walker-Bone
- MRC Versus Arthritis Centre for Musculoskeletal Health and Work, University of Southampton, Southampton, UK
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
| | - A M Dale
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Y Ma
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - G A Colditz
- Department of Surgery, Washington University School of Medicine, St.Louis, MO, USA
| | - B A Evanoff
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| |
Collapse
|
16
|
Abstract
The overlap concentration c* of sodium polystyrene sulfonate in water is calculated using multichain atomistic and coarse grained (CG) simulations for a range of chain lengths. Fully atomistic molecular dynamics simulations are carried out for N = 32-192 monomers. The CG model was parameterized to match the end-to-end distance from the atomistic simulations at small N and allows us to simulate a much larger N. Treating the hydrophobic backbone by inclusion of attraction between monomers is an essential addition to the CG model. The simulation c* are in agreement with experimental data, yet at c*, the chains are not fully stretched, even for N as large as 1200. This implies that none of the experimental systems are in the scaling regime and to reach the scaling regime for NaPSS chains much longer than N = 1200 are required.
Collapse
Affiliation(s)
- Bryce A. Thurston
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Gary S. Grest
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Mark J. Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| |
Collapse
|
17
|
Affiliation(s)
- Jonathan A. Bollinger
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Gary S. Grest
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Mark J. Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Michael Rubinstein
- Mechanical Engineering and Materials Science, Biomedical Engineering, Chemistry, and Physics Departments, Duke University, Durham, North Carolina 27708, United States
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, N21W10 Kita-ku, Sapporo 001-0021, Japan
| |
Collapse
|
18
|
O’Connor JB, Mottlowitz MM, Wagner BD, Boyne KL, Stevens MJ, Robertson CE, Harris JK, Laguna TA. Divergence of bacterial communities in the lower airways of CF patients in early childhood. PLoS One 2021; 16:e0257838. [PMID: 34613995 PMCID: PMC8494354 DOI: 10.1371/journal.pone.0257838] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/10/2021] [Indexed: 11/18/2022] Open
Abstract
Rationale Chronic airway infection and inflammation resulting in progressive, obstructive lung disease is the leading cause of morbidity and mortality in cystic fibrosis. Understanding the lower airway microbiota across the ages can provide valuable insight and potential therapeutic targets. Objectives To characterize and compare the lower airway microbiota in cystic fibrosis and disease control subjects across the pediatric age spectrum. Methods Bronchoalveolar lavage fluid samples from 191 subjects (63 with cystic fibrosis) aged 0 to 21 years were collected along with relevant clinical data. We measured total bacterial load using quantitative polymerase chain reaction and performed 16S rRNA gene sequencing to characterize bacterial communities with species-level sensitivity for select genera. Clinical comparisons were investigated. Measurements and main results Cystic fibrosis samples had higher total bacterial load and lower microbial diversity, with a divergence from disease controls around 2–5 years of age, as well as higher neutrophilic inflammation relative to bacterial burden. Cystic fibrosis samples had increased abundance of traditional cystic fibrosis pathogens and decreased abundance of the Streptococcus mitis species group in older subjects. Interestingly, increased diversity in the heterogeneous disease controls was independent of diagnosis and indication. Sequencing was more sensitive than culture, and antibiotic exposure was more common in disease controls, which showed a negative relationship with load and neutrophilic inflammation. Conclusions Analysis of lower airway samples from people with cystic fibrosis and disease controls across the ages revealed key differences in airway microbiota and inflammation. The divergence in subjects during early childhood may represent a window of opportunity for intervention and additional study.
Collapse
Affiliation(s)
- John B. O’Connor
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, United States of America
- * E-mail:
| | - Madison M. Mottlowitz
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, United States of America
| | - Brandie D. Wagner
- Department of Pediatrics, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Kathleen L. Boyne
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, United States of America
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Mark J. Stevens
- Department of Pediatrics, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Charles E. Robertson
- Department of Pediatrics, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Jonathan K. Harris
- Department of Pediatrics, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Theresa A. Laguna
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, United States of America
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| |
Collapse
|
19
|
Innes-Gold SN, Jacobson DR, Pincus PA, Stevens MJ, Saleh OA. Flexible, charged biopolymers in monovalent and mixed-valence salt: Regimes of anomalous electrostatic stiffening and of salt insensitivity. Phys Rev E 2021; 104:014504. [PMID: 34412211 DOI: 10.1103/physreve.104.014504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 06/21/2021] [Indexed: 11/07/2022]
Abstract
The conformations of biological polyelectrolytes (PEs), such as polysaccharides, proteins, and nucleic acids, affect how they behave and interact with other biomolecules. Relative to neutral polymers, PEs in solution are more locally rigid due to intrachain electrostatic repulsion, the magnitude of which depends on the concentration of added salt. This is typically quantified using the Odijk-Skolnick-Fixman (OSF) electrostatic-stiffening model, in which salt-dependent Debye-Hückel (DH) screening modulates intrachain repulsion. However, the applicability of this approach to flexible PEs has long been questioned. To investigate this, we use high-precision single-molecule elasticity measurements to infer the scaling with salt of the local stiffness of three flexible biopolymers (hyaluronic acid, single-stranded RNA, and single-stranded DNA) in both monovalent and mixed-valence salt solutions. In monovalent salt, we collapse the data across all three polymers by accounting for charge spacing, and find a common power-law scaling of the electrostatic persistence length with ionic strength with an exponent of 0.66±0.02. This result rules out simple OSF pictures of electrostatic stiffening. It is roughly compatible with a modified OSF picture developed by Netz and Orland; alternatively, we posit the exponent can be explained if the relevant electrostatic screening length is the interion spacing rather than the DH length. In mixed salt solutions, we find a regime where adding monovalent salt, in the presence of multivalent salt, does not affect PE stiffness. Using coarse-grained simulations, and a three-state model of condensed, chain-proximate, and bulk ions, we attribute this regime to a "jacket" of ions surrounding the PE that regulates the chain's effective charge density as ionic strength varies. The size of this jacket in simulations is again consistent with a screening length controlled by interion spacing rather than the DH length. Taken together, our results describe a unified picture of the electrostatic stiffness of polyelectrolytes in the mixed-valence salt conditions of direct relevance to cellular and intercellular biological systems.
Collapse
Affiliation(s)
- Sarah N Innes-Gold
- Materials Department, University of California, Santa Barbara, California 93106, USA
| | - David R Jacobson
- Physics Department, University of California, Santa Barbara, California 93106, USA
| | - Philip A Pincus
- Materials Department and Physics Department, University of California, Santa Barbara, California 93106, USA
| | - Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Omar A Saleh
- Materials Department and Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106, USA
| |
Collapse
|
20
|
Abstract
Polymerization induced phase separation (PIPS) in a three component thermoset is studied using molecular dynamics simulations of a new coarse-grained thermoset model. The system includes two crosslinker molecules, which differ in their glass transition temperatures (Tg) and chain length and thus have the potential for phase separation. One crosslinker has a high Tg corresponding to a rubbery behavior, and simulations were performed for a short length (4 beads) and a long length (33 beads). The resin and other crosslinker have low Tg. A coarse-grained model is developed with these features and with interaction parameters determined so that for either rubbery crosslinker length, the system is in the liquid state at the cure temperature. For sufficiently slow reaction rates, the long rubbery molecule exhibits PIPS into a bicontinuous array of nanoscale domains, but the short one does not, reproducing recent experimental results. The simulations demonstrate that the reaction rates must be slow enough to allow diffusion to yield phase separation. Particularly, the reaction rate corresponding to the secondary amine must be very slow, else the structure of crosslinked clusters and the substantially increased diffusion time will prevent PIPS.
Collapse
Affiliation(s)
- Mark J Stevens
- Sandia National Laboratories, Center for Integrated Nanotechnologies, Albuquerque, New Mexico 87185-1315, USA
| |
Collapse
|
21
|
Williamson KM, Wagner BD, Robertson CE, Stevens MJ, Sontag MK, Mourani PM, Harris JK. Modified PCR protocol to increase sensitivity for determination of bacterial community composition. Microbiome 2021; 9:90. [PMID: 33849648 PMCID: PMC8045227 DOI: 10.1186/s40168-020-00958-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND The objective of this project was to increase the sensitivity of sequence-based bacterial community determination without impacting community composition or interfering with cluster formation during sequencing. Two PCR protocols (standard and modified) were examined in airway samples where we observed a large range in bacterial load (3.1-6.2 log10 16S rRNA gene copies/reaction). Tracheal aspirate (TA) samples (n = 99) were collected from sixteen children requiring mechanical ventilation at a single center. DNA was extracted, and total bacterial load (TBL) was assessed using qPCR. Amplification of 16S rRNA was attempted with both protocols in all samples. RESULTS PCR product was observed using both protocols in 52 samples and in 24 additional samples only with the modified protocol. TBL, diversity metrics, and prominent taxa were compared for samples in three groups based on success of the two protocols (successful with both, success with modified only, unsuccessful for both). TBL differed significantly across the three groups (p<0.001). Specifically, the modified protocol allowed amplification from samples with intermediate TBL. Shannon diversity was similar between the two protocols, and Morisita-Horn beta diversity index showed high agreement between the two protocols within samples (median value 0.9997, range 0.9947 to 1). We show that both protocols identify similar communities, and the technical variability of both protocols was very low. The use of limited PCR cycles was a key feature to limit impact of background by exclusion of 24% of samples with no evidence of bacterial DNA present in the sample. CONCLUSION The modified amplification protocol represents a viable approach that increased sensitivity of bacterial community analysis, which is important for study of the human airway microbiome where bacterial load is highly variable. Video abstract.
Collapse
Affiliation(s)
- Kayla M. Williamson
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado School of Medicine, 13001 17th Place, Mail Stop B119, Aurora, CO 80045 USA
| | - Brandie D. Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado School of Medicine, 13001 17th Place, Mail Stop B119, Aurora, CO 80045 USA
- Section of Critical Care, Department of Pediatrics, University of Colorado School of Medicine and Children’s Hospital Colorado, 13123 E. 16th Ave. Box B395, Aurora, CO 80045 USA
| | - Charles E. Robertson
- Division of Infectious Diseases, School of Medicine, University of Colorado, 12700 East 19th Avenue, Mail Stop B168, Aurora, CO 80045 USA
| | - Mark J. Stevens
- Section of Critical Care, Department of Pediatrics, University of Colorado School of Medicine and Children’s Hospital Colorado, 13123 E. 16th Ave. Box B395, Aurora, CO 80045 USA
| | - Marci K. Sontag
- Department of Epidemiology, Colorado School of Public Health, University of Colorado School of Medicine, 13001 17th Place, Mail Stop B119, Aurora, CO 80045 USA
| | - Peter M. Mourani
- Section of Critical Care, Department of Pediatrics, University of Colorado School of Medicine and Children’s Hospital Colorado, 13123 E. 16th Ave. Box B395, Aurora, CO 80045 USA
| | - J. Kirk Harris
- Section of Critical Care, Department of Pediatrics, University of Colorado School of Medicine and Children’s Hospital Colorado, 13123 E. 16th Ave. Box B395, Aurora, CO 80045 USA
| |
Collapse
|
22
|
Khalaf RT, Furuta GT, Wagner BD, Robertson CE, Andrews R, Stevens MJ, Fillon SA, Zemanick ET, Harris JK. Influence of Acid Blockade on the Aerodigestive Tract Microbiome in Children With Cystic Fibrosis. J Pediatr Gastroenterol Nutr 2021; 72:520-527. [PMID: 33394582 PMCID: PMC8315410 DOI: 10.1097/mpg.0000000000003010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Acid blockade is commonly prescribed in patients with cystic fibrosis (CF). Growing concerns, however, exist about its possible role in the pathophysiology of pulmonary infections. We aimed to investigate if acid blockade alters esophageal and respiratory microbiota leading to dysbiosis and inflammation. METHODS We performed a cross sectional study of children with CF who were either prescribed acid blockade or not. Samples from the gastrointestinal and respiratory tracts were obtained and microbiome analyzed. Mixed effect models were used to compare outcomes between cohorts and across sampling sites. A random subject intercept was included to account for the multiple sampling sites per individual. RESULTS A cohort of 25 individuals, 44% girls with median age of 13.8 years [IQR 11.2--14.8] were enrolled. Alpha diversity, total bacterial load, and beta diversity were similar across anatomic compartments, across the upper gastrointestinal tract, and in respiratory samples. Similar alpha diversity, total bacterial load, and beta diversity results were also observed when comparing individuals on versus those off acid blockade. IL-8 was elevated in the distal versus proximal esophagus in the whole cohort (P < 0.01). IL-8 concentrations were similar in the distal esophagus in patients on and off acid blockade, but significantly greater in the proximal esophagus of subjects on treatment (P < 0.01). CONCLUSIONS On the basis of these data, acid blockade use does not appear to influence the microbiome of the aerodigestive tract in children with cystic fibrosis suggesting a complex interplay between these medications and the bacterial composition of the esophagus and lung.
Collapse
Affiliation(s)
- Racha T. Khalaf
- Department of Pediatrics, Gastrointestinal Eosinophilic Diseases Program, Section of Pediatric Gastroenterology, Hepatology and Nutrition, University of Colorado School of Medicine, Digestive Health Institute, Children’s Hospital Colorado, Aurora, CO
- Department of Pediatrics, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Glenn T. Furuta
- Department of Pediatrics, Gastrointestinal Eosinophilic Diseases Program, Section of Pediatric Gastroenterology, Hepatology and Nutrition, University of Colorado School of Medicine, Digestive Health Institute, Children’s Hospital Colorado, Aurora, CO
- Department of Pediatrics, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Brandie D. Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora
| | - Charles E. Robertson
- Department of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Rachel Andrews
- Department of Pediatrics, Gastrointestinal Eosinophilic Diseases Program, Section of Pediatric Gastroenterology, Hepatology and Nutrition, University of Colorado School of Medicine, Digestive Health Institute, Children’s Hospital Colorado, Aurora, CO
| | - Mark J. Stevens
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Sophie A. Fillon
- Department of Pediatrics, Gastrointestinal Eosinophilic Diseases Program, Section of Pediatric Gastroenterology, Hepatology and Nutrition, University of Colorado School of Medicine, Digestive Health Institute, Children’s Hospital Colorado, Aurora, CO
- Mucosal Inflammation Program, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora
- Department of Cancer Immunology and Immune Modulation, Boehringer Ingelheim Pharma GmbH & Co.KG, Biberach, Germany
| | - Edith T. Zemanick
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - J. Kirk Harris
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO
| |
Collapse
|
23
|
Stevens MJ, West S, Gard G, Renaud C, Nevell D, Roderick S, Le A. Utility of adjuvant whole abdominal radiation therapy in ovarian clear cell cancer (OCCC): a pragmatic cohort study of women with classic immuno-phenotypic signature. Radiat Oncol 2021; 16:29. [PMID: 33549120 PMCID: PMC7866446 DOI: 10.1186/s13014-021-01750-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 01/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To evaluate the initial experience and clinical utility of first-line adjuvant intensity-modulated whole abdominal radiation therapy (WART) in women with ovarian clear cell cancer (OCCC) referred to an academic center. METHODS Progression-free and overall survival was analyzed in a pragmatic observational cohort study of histologically pure OCCC patients over-expressing HNF-1ß treated between 2013 and end-December 2018. An in-house intensity-modulated WART program was developed from a published pre-clinical model. Radiation dose-volume data was curated to American Association of Physics in Medicine (AAPM) Task Group 263 recommendations. A dedicated database prospectively recorded presenting characteristics and outcomes in a standardized fashion. RESULTS Five women with FIGO (2018) stage IA to IIIA2 OCCC were treated with first-line WART. Median age was 58 years (range 47-68 years). At diagnosis CA-125 was elevated in 4 cases (median 56 kU/L: range 18.4-370 kU/L) before primary de-bulking surgery. Severe premorbid endometriosis was documented in 3 patients. At a median follow-up of 77 months (range 16-83 mo.), all patients remain alive and progression-free on clinical, biochemical (CA-125), and 18Fluoro-deoxyglucose (FDG) PET/CT re-evaluation. Late radiation toxicity was significant (G3) in 1 case who required a limited bowel resection and chronic nutritional support at 9 months post-WART; 2 further patients had asymptomatic (G2) osteoporotic fragility fractures of axial skeleton at 12 months post-radiation treated with anti-resorptive agents (denosumab). CONCLUSIONS The clinical utility of intensity-modulated WART in OCCC over-expressing HNF-1β was suggested in this small observational cohort study. The hypothesis that HNF-1β is a portent of platinum-resistance and an important predictive biomarker in OCCC needs further confirmation. Curating multi-institutional cohort studies utilizing WART by means of "Big Data" may improve OCCC care standards in the future.
Collapse
Affiliation(s)
- Mark J Stevens
- Department of Radiation Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Level 1 ASB Building, St Leonards, NSW, 2065, Australia. .,Northern Clinical School, University of Sydney, St Leonards, NSW, Australia.
| | - Simon West
- Northern Clinical School, University of Sydney, St Leonards, NSW, Australia.,Department of Obstetrics and Gynecology, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Gregory Gard
- Northern Clinical School, University of Sydney, St Leonards, NSW, Australia.,Department of Obstetrics and Gynecology, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Christopher Renaud
- Department of Pathology, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - David Nevell
- Department of Pathology, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Stephanie Roderick
- Department of Radiation Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Level 1 ASB Building, St Leonards, NSW, 2065, Australia
| | - Andrew Le
- Department of Radiation Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Level 1 ASB Building, St Leonards, NSW, 2065, Australia
| |
Collapse
|
24
|
Priest C, VanGordon MR, Rempe C, Chaudhari MI, Stevens MJ, Rick S, Rempe SB. Computing Potential of the Mean Force Profiles for Ion Permeation Through Channelrhodopsin Chimera, C1C2. Methods Mol Biol 2021; 2191:17-28. [PMID: 32865736 DOI: 10.1007/978-1-0716-0830-2_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Umbrella sampling, coupled with a weighted histogram analysis method (US-WHAM), can be used to construct potentials of mean force (PMFs) for studying the complex ion permeation pathways of membrane transport proteins. Despite the widespread use of US-WHAM, obtaining a physically meaningful PMF can be challenging. Here, we provide a protocol to resolve that issue. Then, we apply that protocol to compute a meaningful PMF for sodium ion permeation through channelrhodopsin chimera, C1C2, for illustration.
Collapse
Affiliation(s)
- Chad Priest
- Sandia National Laboratories, Albuquerque, NM, USA
| | - Monika R VanGordon
- Department of Chemistry, University of New Orleans, New Orleans, LA, USA
| | | | | | | | - Steve Rick
- Department of Chemistry, University of New Orleans, New Orleans, LA, USA
| | | |
Collapse
|
25
|
Paren BA, Thurston BA, Neary WJ, Kendrick A, Kennemur JG, Stevens MJ, Frischknecht AL, Winey KI. Percolated Ionic Aggregate Morphologies and Decoupled Ion Transport in Precise Sulfonated Polymers Synthesized by Ring-Opening Metathesis Polymerization. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01906] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Benjamin A. Paren
- Dept. Of Materials Science & Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6272, United States
| | - Bryce A. Thurston
- Center for Integrated Nanotechnologies, Sandia National Labs, Albuquerque, New Mexico 87185-1411, United States
| | - William J. Neary
- Dept. Of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Aaron Kendrick
- Dept. Of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Justin G. Kennemur
- Dept. Of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Mark J. Stevens
- Center for Integrated Nanotechnologies, Sandia National Labs, Albuquerque, New Mexico 87185-1411, United States
| | - Amalie L. Frischknecht
- Center for Integrated Nanotechnologies, Sandia National Labs, Albuquerque, New Mexico 87185-1411, United States
| | - Karen I. Winey
- Dept. Of Materials Science & Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6272, United States
| |
Collapse
|
26
|
Abstract
We calculate the solvation energy of monovalent and divalent ions in various liquids with coarse-grained molecular dynamics simulations. Our theory treats the solvent as a Stockmayer fluid, which accounts for the intrinsic dipole moment of molecules and the rotational dynamics of the dipoles. Despite the simplicity of the model, we obtain qualitative agreement between the simulations and experimental data for the free energy and enthalpy of ion solvation, which indicates that the primary contribution to the solvation energy arises mainly from the first and possibly second solvation shells near the ions. Our results suggest that a Stockmayer fluid can serve as a reference model that enables direct comparison between theory and experiment and may be invoked to scale up electrostatic interactions from the atomic to the molecular length scale.
Collapse
Affiliation(s)
- Cameron J Shock
- Department of Physics, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Amalie L Frischknecht
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Issei Nakamura
- Department of Physics, Michigan Technological University, Houghton, Michigan 49931, United States
| |
Collapse
|
27
|
Abstract
Single-ion conducting polymers such as ionomers are promising battery electrolyte materials, but it is critical to understand how rates and mechanisms of free cation transport depend on the nanoscale aggregation of cations and polymer-bound anions. We perform coarse-grained molecular dynamics simulations of ionomer melts to understand cation mobility as a function of polymer architecture, background relative permittivity, and corresponding ionic aggregate morphology. In systems exhibiting percolated ionic aggregates, cations diffuse via stepping motions along the ionic aggregates. These diffusivities can be quantitatively predicted by calculating the lifetimes of continuous association between oppositely charged ions, which equal the time scales of the stepping (diffusive) motions. In contrast, predicting cation diffusivity for systems with isolated ionic aggregates requires another time scale. Our results suggest that to improve conductivity the Coulombic interaction strength should be strong enough to favor percolated aggregates but weak enough to facilitate ion dissociation.
Collapse
Affiliation(s)
- Jonathan A. Bollinger
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Mark J. Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Amalie L. Frischknecht
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| |
Collapse
|
28
|
Bachand GD, Bollinger JA, Imam Z, Stevens MJ. GMPCPP-Tubulin Islands Regulate the Mechanism and Kinetics of Microtubule Depolymerization. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.3227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
29
|
Innes-Gold SN, Pincus PA, Stevens MJ, Saleh OA. Polyelectrolyte Conformation Controlled by a Trivalent-Rich Ion Jacket. Phys Rev Lett 2019; 123:187801. [PMID: 31763890 DOI: 10.1103/physrevlett.123.187801] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 08/02/2019] [Indexed: 06/10/2023]
Abstract
The configuration of charged polymers is heavily dependent on interactions with surrounding salt ions, typically manifesting as a sensitivity to the bulk ionic strength. Here, we use single-molecule mechanical measurements to show that a charged polysaccharide, hyaluronic acid, shows a surprising regime of insensitivity to ionic strength in the presence of trivalent ions. Using simulations and theory, we propose that this is caused by the formation of a "jacket" of ions, tightly associated with the polymer, whose charge (and thus effect on configuration) is robust against changes in solution composition.
Collapse
Affiliation(s)
- Sarah N Innes-Gold
- Materials Department, University of California, Santa Barbara, California 93106, USA
| | - Philip A Pincus
- Materials Department and Physics Department, University of California, Santa Barbara, California 93106, USA
| | - Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185-1315, USA
| | - Omar A Saleh
- Materials Department and BMSE program, University of California, Santa Barbara, California 93106, USA
| |
Collapse
|
30
|
Bollinger JA, Stevens MJ. Diverse balances of tubulin interactions and shape change drive and interrupt microtubule depolymerization. Soft Matter 2019; 15:8137-8146. [PMID: 31593193 DOI: 10.1039/c9sm01323g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Microtubules are stiff biopolymers that self-assemble via the addition of GTP-tubulin (αβ-dimer bound to GTP), but hydrolysis of GTP- to GDP-tubulin within the tubules destabilizes them toward catastrophically-fast depolymerization. The molecular mechanisms and features of the individual tubulin proteins that drive such behavior are still not well-understood. Using molecular dynamics simulations of whole microtubules built from a coarse-grained model of tubulin, we demonstrate how conformational shape changes (i.e., deformations) in subunits that frustrate tubulin-tubulin binding within microtubules drive depolymerization of stiff tubules via unpeeling "ram's horns" consistent with experiments. We calculate the sensitivity of these behaviors to the length scales and strengths of binding attractions and varying degrees of binding frustration driven by subunit shape change, and demonstrate that the dynamic instability and mechanical properties of microtubules can be produced based on either balanced or imbalanced strengths of lateral and vertical binding attractions. Finally, we show how catastrophic depolymerization can be interrupted by small regions of the microtubule containing undeformed dimers, corresponding to incomplete lattice hydrolysis. The results demonstrate a mechanism by which microtubule rescue can occur.
Collapse
Affiliation(s)
- Jonathan A Bollinger
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
| | - Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
| |
Collapse
|
31
|
Horsley PJ, Perera L, Veness MJ, Stevens MJ, Eade TN, Back M, Brown C, Jayamanne DT. Outcomes for elderly patients 75 years and older treated with curative intent radiotherapy for mucosal squamous cell carcinomas of the head and neck. Head Neck 2019; 42:25-32. [DOI: 10.1002/hed.25969] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 08/06/2019] [Accepted: 09/06/2019] [Indexed: 11/08/2022] Open
Affiliation(s)
- Patrick J. Horsley
- Radiation Oncology DepartmentNorthern Sydney Cancer Centre, Royal North Shore Hospital St Leonards New South Wales Australia
| | - Lakmalie Perera
- Radiation Oncology DepartmentCrown Princess Mary Cancer Centre, Westmead Hospital Westmead New South Wales Australia
| | - Michael J. Veness
- Radiation Oncology DepartmentCrown Princess Mary Cancer Centre, Westmead Hospital Westmead New South Wales Australia
- University of Sydney Sydney New South Wales Australia
| | - Mark J. Stevens
- Radiation Oncology DepartmentNorthern Sydney Cancer Centre, Royal North Shore Hospital St Leonards New South Wales Australia
| | - Thomas N. Eade
- Radiation Oncology DepartmentNorthern Sydney Cancer Centre, Royal North Shore Hospital St Leonards New South Wales Australia
| | - Michael Back
- Radiation Oncology DepartmentNorthern Sydney Cancer Centre, Royal North Shore Hospital St Leonards New South Wales Australia
| | - Chris Brown
- NHMRC Clinical Trials Centre, University of Sydney Camperdown Australia
| | - Dasantha T. Jayamanne
- Radiation Oncology DepartmentNorthern Sydney Cancer Centre, Royal North Shore Hospital St Leonards New South Wales Australia
| |
Collapse
|
32
|
Stevens MJ, Walker-Bone K, Culliford DJ, Alcacer-Pitarch B, Blake A, Hopkinson N, Teh LS, Vital EM, Edwards CJ, Williams AE, Cherry L. Work participation, mobility and foot symptoms in people with systemic lupus erythematosus: findings of a UK national survey. J Foot Ankle Res 2019; 12:26. [PMID: 31164925 PMCID: PMC6489339 DOI: 10.1186/s13047-019-0335-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 04/11/2019] [Indexed: 11/12/2022] Open
Abstract
Objective The aim of this study was to investigate whether foot and lower limb related symptoms were associated with work participation and poor mobility in people with Systemic Lupus Erythematosus (SLE). Method A quantitative, cross-sectional, self-reported survey design was utilised. People with SLE from six United Kingdom (UK) treatment centres and a national register were invited to complete a survey about lower limb and foot health, work participation and mobility. Data collected included work status and the prevalence of foot symptoms. The focus of the analyses was to explore potential associations between poor foot health work non-participation. Results In total, 182 useable surveys were returned. Seventy-nine respondents reported themselves as employed and 32 reported work non-participation. The remaining were retired due to age or reported work non-participation for other reasons. Work non-participation due to foot symptoms was significantly associated with difficulty walking (p = 0.024), past episodes of foot swelling (p = 0.041), and past episodes of foot ulceration (p = 0.018). There was a significant increase in foot disability scores amongst those not working (mean 18.13, 95% CI: 14.85–21.41) compared to those employed (mean 10.16, 95% CI: 8.11–12.21). Conclusions Twenty-nine% of people with SLE reported work non-participation because of lower limb or foot problems. Our results suggest that foot health and mobility may be important contributors to a persons’ ability to remain in work and should be considered as part of a clinical assessment.
Collapse
Affiliation(s)
- M J Stevens
- 1MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.,Arthritis Research UK/MRC Centre for Musculoskeletal Health and Work, Southampton, UK
| | - K Walker-Bone
- 1MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.,Arthritis Research UK/MRC Centre for Musculoskeletal Health and Work, Southampton, UK
| | - D J Culliford
- 3Methodological Hub, NIHR Collaboration for Applied Health Research and Care Wessex, University of Southampton, Southampton, UK
| | - B Alcacer-Pitarch
- 4NIHR Leeds Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust and Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - A Blake
- Private podiatrist, Verwood, Dorset UK
| | - N Hopkinson
- 6Department of Rheumatology, Royal Bournemouth and Christchurch Hospitals NHS Foundation Trust, Bournemouth, UK
| | - L S Teh
- 7Department of Rheumatology, Royal Blackburn Teaching Hospital, East Lancashire Hospital NHS Trust, Blackburn, UK.,8Faculty of Clinical and Biomedical Sciences, University of Central Lancashire, Preston, UK
| | - E M Vital
- 4NIHR Leeds Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust and Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - C J Edwards
- 9NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - A E Williams
- 10Directorate of prosthetics, orthotics and Podiatry, University of Salford, Salford, UK
| | - L Cherry
- 11School of Health Sciences, Faculty of Health Sciences, University of Southampton, Building 45, Burgess Road, Southampton, SO17 1BJ UK.,12Department of Podiatry, Solent NHS Trust, Southampton, UK
| |
Collapse
|
33
|
Abstract
Curative-intent lung cancer radiation therapy either alone (RT) or combined with immuno-chemotherapy is associated with potential risk of serious radiation-induced lung injury. This review provides a summary of the role of SPECT ventilation perfusion (V/Q) imaging as an emerging adjunct to lung cancer RT planning and treatment dosimetry. Denoted "functional lung avoidance RT" it is hypothesized that preferential dosimetric avoidance of physiologically functional lung may reduce the frequency of radiation-induced lung injury. SPECT V/Q imaging datasets available during the planning process allows the prioritization (or "personalization') of RT dose to minimize the volume of functional lung probabilistically exposed to injurious radiation dose. Selective escalation of target dose and adaptive planning and replanning is also enabled. The emergent importance of the tumor-lung microenvironment and its biologic relationship to local immune effectors in lung cancer provides further incentive to individualize RT planning and delivery. This review examines important normal tissue dosimetric constraints that are part of current standards-of-care and the new dosimetric parameters associated with functional lung avoidance RT. SPECT V/Q has been a valuable tool in investigating the feasibility and efficacy of functional lung avoidance RT but is yet to become main stream due to the lack of large clinical trials. It is encouraging however that functional lung avoidance is feasible in RT dose-target delineation and some of the more promising studies are discussed.
Collapse
Affiliation(s)
- Enid M Eslick
- Department of Nuclear Medicine, Royal North Shore Hospital, Sydney, NSW, Australia; Faculty of Health Sciences, University of Sydney, Sydney, NSW, Australia
| | - Mark J Stevens
- Northern Sydney Cancer Centre, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Dale L Bailey
- Department of Nuclear Medicine, Royal North Shore Hospital, Sydney, NSW, Australia; Faculty of Health Sciences, University of Sydney, Sydney, NSW, Australia.
| |
Collapse
|
34
|
Affiliation(s)
- Mark J. Stevens
- Sandia National Laboratories, Center for Integrated Nanotechnologies, Albuquerque, New Mexico 87185-1315, USA
| |
Collapse
|
35
|
Stevens MJ, Berezney JP, Saleh OA. The effect of chain stiffness and salt on the elastic response of a polyelectrolyte. J Chem Phys 2018; 149:163328. [DOI: 10.1063/1.5035340] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mark J. Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, P.O. Box 5800, MS 1315, Albuquerque, New Mexico 87185-1315, USA
| | - John P. Berezney
- Materials Department and BMSE Program, University of California, Santa Barbara, California 93106, USA
| | - Omar A. Saleh
- Materials Department and BMSE Program, University of California, Santa Barbara, California 93106, USA
| |
Collapse
|
36
|
Trigg EB, Gaines TW, Maréchal M, Moed DE, Rannou P, Wagener KB, Stevens MJ, Winey KI. Self-assembled highly ordered acid layers in precisely sulfonated polyethylene produce efficient proton transport. Nat Mater 2018; 17:725-731. [PMID: 29807986 DOI: 10.1038/s41563-018-0097-2] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/30/2018] [Indexed: 05/21/2023]
Abstract
Recent advances in polymer synthesis have allowed remarkable control over chain microstructure and conformation. Capitalizing on such developments, here we create well-controlled chain folding in sulfonated polyethylene, leading to highly uniform hydrated acid layers of subnanometre thickness with high proton conductivity. The linear polyethylene contains sulfonic acid groups pendant to precisely every twenty-first carbon atom that induce tight chain folds to form the hydrated layers, while the methylene segments crystallize. The proton conductivity is on par with Nafion 117, the benchmark for fuel cell membranes. We demonstrate that well-controlled hairpin chain folding can be utilized for proton conductivity within a crystalline polymer structure, and we project that this structure could be adapted for ion transport. This layered polyethylene-based structure is an innovative and versatile design paradigm for functional polymer membranes, opening doors to efficient and selective transport of other ions and small molecules on appropriate selection of functional groups.
Collapse
Affiliation(s)
- Edward B Trigg
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Taylor W Gaines
- The George and Josephine Butler Polymer Research Laboratory, Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Manuel Maréchal
- Univ. Grenoble Alpes, CNRS, CEA, INAC-SyMMES, Grenoble, France
| | - Demi E Moed
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Patrice Rannou
- Univ. Grenoble Alpes, CNRS, CEA, INAC-SyMMES, Grenoble, France
| | - Kenneth B Wagener
- The George and Josephine Butler Polymer Research Laboratory, Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM, USA
| | - Karen I Winey
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
37
|
Abstract
Young's elastic modulus and the persistence length are calculated for a coarse-grained model of tubule forming polymers. The model uses a wedge shaped composite of particles that previously has been shown to self-assemble into tubules. These calculations demonstrate that the model yields very large persistence lengths (corresponding to 78-126 μm) that are comparable to that observed in experiments for the microtubule lengths accessible to the calculations. The source for the stiffness is the restricted rotation of the monomer due to the excluded volume interactions between bonded macromolecular monomers as well as the binding between monomers. For this reason, large persistence lengths are common in tubule systems with a macromolecule as the monomer. The persistence length increases linearly with increased binding strength in the filament direction. No dependence in the persistence length is found for varying the tubule pitch for geometries with the protofilaments remaining straight.
Collapse
Affiliation(s)
- Mark J Stevens
- Sandia National Laboratories, Center for Integrated Nanotechnologies, Albuquerque, New Mexico 87185-1315, USA
| |
Collapse
|
38
|
Abstract
Microtubules exhibit a dynamic instability between growth and catastrophic depolymerization. GTP-tubulin (αβ-dimer bound to GTP) self-assembles, but dephosphorylation of GTP- to GDP-tubulin within the tubule results in destabilization. While the mechanical basis for destabilization is not fully understood, one hypothesis is that dephosphorylation causes tubulin to change shape, frustrating bonds and generating stress. To test this idea, we perform molecular dynamics simulations of microtubules built from coarse-grained models of tubulin, incorporating a small compression of α-subunits associated with dephosphorylation in experiments. We find that this shape change induces depolymerization of otherwise stable systems via unpeeling "ram's horns" characteristic of microtubules. Depolymerization can be averted by caps with uncompressed α-subunits, i.e., GTP-rich end regions. Thus, the shape change is sufficient to yield microtubule behavior.
Collapse
Affiliation(s)
- Jonathan A Bollinger
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque NM 87185, USA.
| | | |
Collapse
|
39
|
Bollinger JA, Stevens MJ. Catastrophic Depolymerization of Microtubules Driven by Subunit Shape Change. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
40
|
Affiliation(s)
- Shengfeng Cheng
- Department of Physics, Center for Soft Matter and Biological Physics, and Macromolecules Innovation Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Mark J. Stevens
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Gary S. Grest
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| |
Collapse
|
41
|
Abstract
The role of an external field on capillary waves at the liquid-vapor interface of a dipolar fluid is investigated using molecular dynamics simulations. For fields parallel to the interface, the interfacial width squared increases linearly with respect to the logarithm of the size of the interface across all field strengths tested. The value of the slope decreases with increasing field strength, indicating that the field dampens the capillary waves. With the inclusion of the parallel field, the surface stiffness increases with increasing field strength faster than the surface tension. For fields perpendicular to the interface, the interfacial width squared is linear with respect to the logarithm of the size of the interface for small field strengths, and the surface stiffness is less than the surface tension. Above a critical field strength that decreases as the size of the interface increases, the interface becomes unstable due to the increased amplitude of the capillary waves.
Collapse
Affiliation(s)
- Jason P Koski
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Stan G Moore
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Gary S Grest
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Mark J Stevens
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| |
Collapse
|
42
|
Leroue MK, Harris JK, Burgess KM, Stevens MJ, Miller JI, Sontag MK, Sierra YL, Wagner BD, Mourani PM. Molecular analysis of endotracheal tube biofilms and tracheal aspirates in the pediatric intensive care unit. Adv Pediatr Res 2017; 4:14. [PMID: 29963643 PMCID: PMC6023549 DOI: 10.12715/apr.2017.4.14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND Ventilator-associated pneumonia (VAP) is a known complication of mechanically ventilated children in the pediatric intensive care unit (PICU). Endotracheal tube (ETT) biofilms are often implicated in the development of VAP by providing a conduit for pathogens to the lower respiratory tract. METHODS A prospective cohort study from April 2010-March 2011 of children 4 weeks to 18 years of age ventilated for greater than 72 hours to determine the microbiota of ETT biofilms and tracheal aspirates. RESULTS Thirty-three patients were included with a mean age of 6.1 years (SD ± 5.1 years) and average length of intubation of 8.8 days (SD ± 5.0 days). Bacterial communities from tracheal aspirates and the proximal and distal ends of ETTs were determined using 16S rRNA gene libraries. Statistical analysis utilized two-part statistics and the Wilcoxon signed rank sum test for comparison of bacterial communities. Sequencing revealed a predominance of oropharyngeal microbiota including Prevotella and Streptococcus spp. Pathogenic bacterial genera including Staphylococcus, Burkholderia, Moraxella, and Haemophilus were also represented. Bacterial load was greatest at the proximal aspect of the ETT. Duration of intubation did not significantly impact bacterial load. Morisita Horn analysis across sites showed similar communities in 24/33 (72%) of patients. CONCLUSIONS ETT biofilms and tracheal aspirates of intubated patients in the PICU primarily consisted of oropharyngeal microbiota, but had a significant representation of potentially pathogenic genera. While the majority of patients had similar microbiota when comparing their ETT biofilms and tracheal aspirates, a subset of patients showed a divergence between communities that requires further investigation.
Collapse
Affiliation(s)
- Matthew K. Leroue
- Department of Pediatrics, Section of Emergency Medicine, University
of Colorado School of Medicine, Anschutz Medical Center, and Children’s
Hospital Colorado, Aurora, CO, USA
| | - J. Kirk Harris
- Department of Pediatrics, Section of Pulmonary Medicine, University
of Colorado School of Medicine, Anschutz Medical Center, and Children’s
Hospital Colorado, Aurora, CO, USA
| | - Katherine M. Burgess
- Department of Epidemiology, Colorado School of Public Health,
Anschutz Medical Center, Colorado School of Public Health, Aurora, CO, USA
| | - Mark J. Stevens
- Department of Pediatrics, Section of Pulmonary Medicine, University
of Colorado School of Medicine, Anschutz Medical Center, and Children’s
Hospital Colorado, Aurora, CO, USA
| | - Joshua I. Miller
- Department of Epidemiology, Colorado School of Public Health,
Anschutz Medical Center, Colorado School of Public Health, Aurora, CO, USA
| | - Marci K. Sontag
- Department of Epidemiology, Colorado School of Public Health,
Anschutz Medical Center, Colorado School of Public Health, Aurora, CO, USA
| | | | - Brandie D. Wagner
- Department of Biostatistics and Informatics, Colorado School of
Public Health, Aurora, CO, USA
| | - Peter M. Mourani
- Department of Pediatrics, Section of Critical Care, University of
Colorado School of Medicine, Anschutz Medical Center, and Children’s
Hospital Colorado, Aurora, CO, USA
| |
Collapse
|
43
|
Zemanick ET, Wagner BD, Robertson CE, Ahrens RC, Chmiel JF, Clancy JP, Gibson RL, Harris WT, Kurland G, Laguna TA, McColley SA, McCoy K, Retsch-Bogart G, Sobush KT, Zeitlin PL, Stevens MJ, Accurso FJ, Sagel SD, Harris JK. Airway microbiota across age and disease spectrum in cystic fibrosis. Eur Respir J 2017; 50:50/5/1700832. [PMID: 29146601 DOI: 10.1183/13993003.00832-2017] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 08/10/2017] [Indexed: 01/20/2023]
Abstract
Our objectives were to characterise the microbiota in cystic fibrosis (CF) bronchoalveolar lavage fluid (BALF), and determine its relationship to inflammation and disease status.BALF from paediatric and adult CF patients and paediatric disease controls undergoing clinically indicated bronchoscopy was analysed for total bacterial load and for microbiota by 16S rDNA sequencing.We examined 191 BALF samples (146 CF and 45 disease controls) from 13 CF centres. In CF patients aged <2 years, nontraditional taxa (e.gStreptococcus, Prevotella and Veillonella) constituted ∼50% of the microbiota, whereas in CF patients aged ≥6 years, traditional CF taxa (e.gPseudomonas, Staphylococcus and Stenotrophomonas) predominated. Sequencing detected a dominant taxon not traditionally associated with CF (e.gStreptococcus or Prevotella) in 20% of CF BALF and identified bacteria in 24% of culture-negative BALF. Microbial diversity and relative abundance of Streptococcus, Prevotella and Veillonella were inversely associated with airway inflammation. Microbiota communities were distinct in CF compared with disease controls, but did not differ based on pulmonary exacerbation status in CF.The CF microbiota detected in BALF differs with age. In CF patients aged <2 years, Streptococcus predominates, whereas classic CF pathogens predominate in most older children and adults.
Collapse
Affiliation(s)
| | - Brandie D Wagner
- University of Colorado School of Medicine, Aurora, CO, USA.,Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | | | | | - James F Chmiel
- Case Western Reserve University School of Medicine, Rainbow Babies and Children's Hospital, Cleveland, OH, USA
| | - John P Clancy
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ronald L Gibson
- University of Washington, Seattle Children's Hospital, Seattle, WA, USA
| | | | | | | | - Susanna A McColley
- Ann and Robert H. Lurie Children's Hospital of Chicago and Northwestern University, Chicago, IL, USA
| | - Karen McCoy
- Nationwide Children's Hospital, Columbus, OH, USA
| | | | | | | | - Mark J Stevens
- University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Scott D Sagel
- University of Colorado School of Medicine, Aurora, CO, USA
| | - J Kirk Harris
- University of Colorado School of Medicine, Aurora, CO, USA
| |
Collapse
|
44
|
Hull NM, Holinger EP, Ross KA, Robertson CE, Harris JK, Stevens MJ, Pace NR. Longitudinal and Source-to-Tap New Orleans, LA, U.S.A. Drinking Water Microbiology. Environ Sci Technol 2017; 51:4220-4229. [PMID: 28296394 DOI: 10.1021/acs.est.6b06064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The two municipal drinking water systems of New Orleans, LA, U.S.A. were sampled to compare the microbiology of independent systems that treat the same surface water from the Mississippi River. To better understand temporal trends and sources of microbiology delivered to taps, these treatment plants and distribution systems were subjected to source-to-tap sampling over four years. Both plants employ traditional treatment by chloramination, applied during or after settling, followed by filtration before distribution in a warm, low water age system. Longitudinal samples indicated microbiology to have stability both spatially and temporally, and between treatment plants and distribution systems. Disinfection had the greatest impact on microbial composition, which was further refined by filtration and influenced by distribution and premise plumbing. Actinobacteria spp. exhibited trends with treatment. In particular, Mycobacterium spp., very low in finished waters, occurred idiosyncratically at high levels in some tap waters, indicating distribution and/or premise plumbing as main contributors of mycobacteria. Legionella spp., another genus containing potential opportunistic pathogens, also occurred ubiquitously. Source water microbiology was most divergent from tap water, and each step of treatment brought samples more closely similar to tap waters.
Collapse
Affiliation(s)
- Natalie M Hull
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado , Boulder, Colorado 80309, United States
| | - Eric P Holinger
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado , Boulder, Colorado 80309, United States
| | - Kimberly A Ross
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado , Boulder, Colorado 80309, United States
| | - Charles E Robertson
- Division of Infectious Disease, University of Colorado School of Medicine , Anschutz Campus, Aurora, Colorado 80045, United States
| | - J Kirk Harris
- Department of Pediatrics, University of Colorado School of Medicine , Anschutz Campus, Aurora, Colorado 80045, United States
| | - Mark J Stevens
- Department of Pediatrics, University of Colorado School of Medicine , Anschutz Campus, Aurora, Colorado 80045, United States
| | - Norman R Pace
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado , Boulder, Colorado 80309, United States
| |
Collapse
|
45
|
Trigg EB, Stevens MJ, Winey KI. Chain Folding Produces a Multilayered Morphology in a Precise Polymer: Simulations and Experiments. J Am Chem Soc 2017; 139:3747-3755. [DOI: 10.1021/jacs.6b12817] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Edward B. Trigg
- Department
of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Mark J. Stevens
- Center
for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Karen I. Winey
- Department
of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
46
|
Laguna TA, Wagner BD, Williams CB, Stevens MJ, Robertson CE, Welchlin CW, Moen CE, Zemanick ET, Harris JK. Airway Microbiota in Bronchoalveolar Lavage Fluid from Clinically Well Infants with Cystic Fibrosis. PLoS One 2016; 11:e0167649. [PMID: 27930727 PMCID: PMC5145204 DOI: 10.1371/journal.pone.0167649] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/17/2016] [Indexed: 12/15/2022] Open
Abstract
Background Upper airway cultures guide the identification and treatment of lung pathogens in infants with cystic fibrosis (CF); however, this may not fully reflect the spectrum of bacteria present in the lower airway. Our objectives were to characterize the airway microbiota using bronchoalveolar lavage fluid (BALF) from asymptomatic CF infants during the first year of life and to investigate the relationship between BALF microbiota, standard culture and clinical characteristics. Methods BALF, nasopharyngeal (NP) culture and infant pulmonary function testing data were collected at 6 months and one year of age during periods of clinical stability from infants diagnosed with CF by newborn screening. BALF was analyzed for total bacterial load by qPCR and for bacterial community composition by 16S ribosomal RNA sequencing. Clinical characteristics and standard BALF and NP culture results were recorded over five years of longitudinal follow-up. Results 12 BALF samples were collected from 8 infants with CF. Streptococcus, Burkholderia, Prevotella, Haemophilus, Porphyromonas, and Veillonella had the highest median relative abundance in infant CF BALF. Two of the 3 infants with repeat BALF had changes in their microbial communities over six months (Morisita-Horn diversity index 0.36, 0.38). Although there was excellent percent agreement between standard NP and BALF cultures, these techniques did not routinely detect all bacteria identified by sequencing. Conclusions BALF in asymptomatic CF infants contains complex microbiota, often missed by traditional culture of airway secretions. Anaerobic bacteria are commonly found in the lower airways of CF infants.
Collapse
Affiliation(s)
- Theresa A. Laguna
- Department of Pediatrics, University of Minnesota School of Medicine and the Masonic Children’s Hospital, Minneapolis, Minnesota, United States of America
- * E-mail:
| | - Brandie D. Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Cynthia B. Williams
- Department of Pediatrics, University of Minnesota School of Medicine and the Masonic Children’s Hospital, Minneapolis, Minnesota, United States of America
| | - Mark J. Stevens
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Charles E. Robertson
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Cole W. Welchlin
- Department of Pediatrics, University of Minnesota School of Medicine and the Masonic Children’s Hospital, Minneapolis, Minnesota, United States of America
| | - Catherine E. Moen
- Department of Pediatrics, University of Minnesota School of Medicine and the Masonic Children’s Hospital, Minneapolis, Minnesota, United States of America
| | - Edith T. Zemanick
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Jonathan K. Harris
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| |
Collapse
|
47
|
Abstract
Specific ion binding by carboxylates (-COO-) is a broadly important topic because -COO- is one of the most common functional groups coordinated to metal ions in metalloproteins and synthetic polymers. We apply quantum chemical methods and the quasi-chemical free-energy theory to investigate how variations in the number of -COO- ligands in a binding site determine ion-binding preferences. We study a series of monovalent (Li+, Na+, K+, Cs+) and divalent (Zn2+, Ca2+) ions relevant to experimental work on ion channels and ionomers. Of two competing hypotheses, our results support the ligand field strength hypothesis and follow the reverse Hofmeister series for ion solvation and ion transfer from aqueous solution to binding sites with the preferred number of ligands. New insight arises from the finding that ion-binding sequences can be manipulated and even reversed just by constraining the number of carboxylate ligands in the binding sites. Our results help clarify the discrepancy in ion association between molecular ligands in aqueous solutions and ionomers, and their chemical analogues in ion-channel binding sites.
Collapse
Affiliation(s)
- Mark J Stevens
- Center for Integrated Nanotechnologies and ‡Biological and Engineering Sciences, Sandia National Laboratories , Albuquerque, New Mexico 87185, United States
| | - Susan L B Rempe
- Center for Integrated Nanotechnologies and ‡Biological and Engineering Sciences, Sandia National Laboratories , Albuquerque, New Mexico 87185, United States
| |
Collapse
|
48
|
Ting CL, Sorensen-Unruh KE, Stevens MJ, Frischknecht AL. Nonequilibrium simulations of model ionomers in an oscillating electric field. J Chem Phys 2016; 145:044902. [PMID: 27475392 DOI: 10.1063/1.4959120] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
| | | | - Mark J. Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Amalie L. Frischknecht
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| |
Collapse
|
49
|
Stanish LF, Hull NM, Robertson CE, Harris JK, Stevens MJ, Spear JR, Pace NR. Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA. PLoS One 2016; 11:e0157966. [PMID: 27362708 PMCID: PMC4928833 DOI: 10.1371/journal.pone.0157966] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 06/08/2016] [Indexed: 12/29/2022] Open
Abstract
The composition and metabolic activities of microbes in drinking water distribution systems can affect water quality and distribution system integrity. In order to understand regional variations in drinking water microbiology in the upper Ohio River watershed, the chemical and microbiological constituents of 17 municipal distribution systems were assessed. While sporadic variations were observed, the microbial diversity was generally dominated by fewer than 10 taxa, and was driven by the amount of disinfectant residual in the water. Overall, Mycobacterium spp. (Actinobacteria), MLE1-12 (phylum Cyanobacteria), Methylobacterium spp., and sphingomonads were the dominant taxa. Shifts in community composition from Alphaproteobacteria and Betaproteobacteria to Firmicutes and Gammaproteobacteria were associated with higher residual chlorine. Alpha- and beta-diversity were higher in systems with higher chlorine loads, which may reflect changes in the ecological processes structuring the communities under different levels of oxidative stress. These results expand the assessment of microbial diversity in municipal distribution systems and demonstrate the value of considering ecological theory to understand the processes controlling microbial makeup. Such understanding may inform the management of municipal drinking water resources.
Collapse
Affiliation(s)
- Lee F. Stanish
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, United States of America
- * E-mail:
| | - Natalie M. Hull
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, United States of America
| | - Charles E. Robertson
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, United States of America
| | - J. Kirk Harris
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Mark J. Stevens
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - John R. Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States of America
| | - Norman R. Pace
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, United States of America
| |
Collapse
|
50
|
Salerno KM, Frischknecht AL, Stevens MJ. Charged Nanoparticle Attraction in Multivalent Salt Solution: A Classical-Fluids Density Functional Theory and Molecular Dynamics Study. J Phys Chem B 2016; 120:5927-37. [DOI: 10.1021/acs.jpcb.6b01392] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K. Michael Salerno
- Center
for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Amalie L. Frischknecht
- Center
for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Mark J. Stevens
- Center
for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| |
Collapse
|