Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 31
Filter
1.
ACS Energy Lett ; 8(1): 250-258, 2023 Jan 13.
Article in English | MEDLINE | ID: mdl-36660372

ABSTRACT

Band gap tunability of lead mixed halide perovskites makes them promising candidates for various applications in optoelectronics. Here we use the localization landscape theory to reveal that the static disorder due to iodide:bromide compositional alloying contributes at most 3 meV to the Urbach energy. Our modeling reveals that the reason for this small contribution is due to the small effective masses in perovskites, resulting in a natural length scale of around 20 nm for the "effective confining potential" for electrons and holes, with short-range potential fluctuations smoothed out. The increase in Urbach energy across the compositional range agrees well with our optical absorption measurements. We model systems of sizes up to 80 nm in three dimensions, allowing us to accurately reproduce the experimentally observed absorption spectra of perovskites with halide segregation. Our results suggest that we should look beyond static contribution and focus on the dynamic temperature dependent contribution to the Urbach energy.

2.
PLoS One ; 15(5): e0228606, 2020.
Article in English | MEDLINE | ID: mdl-32392246

ABSTRACT

Bordetella pertussis, the causative agent of whopping cough, produces an adenylate cyclase toxin (CyaA) that plays a key role in the host colonization by targeting innate immune cells which express CD11b/CD18, the cellular receptor of CyaA. CyaA is also able to invade non-phagocytic cells, via a unique entry pathway consisting in a direct translocation of its catalytic domain across the cytoplasmic membrane of the cells. Within the cells, CyaA is activated by calmodulin to produce high levels of cyclic adenosine monophosphate (cAMP) and alter cellular physiology. In this study, we explored the effects of CyaA toxin on the cellular and molecular structure remodeling of A549 alveolar epithelial cells. Using classical imaging techniques, biochemical and functional tests, as well as advanced cell mechanics method, we quantify the structural and functional consequences of the massive increase of intracellular cyclic AMP induced by the toxin: cell shape rounding associated to adhesion weakening process, actin structure remodeling for the cortical and dense components, increase in cytoskeleton stiffness, and inhibition of migration and repair. We also show that, at low concentrations (0.5 nM), CyaA could significantly impair the migration and wound healing capacities of the intoxicated alveolar epithelial cells. As such concentrations might be reached locally during B. pertussis infection, our results suggest that the CyaA, beyond its major role in disabling innate immune cells, might also contribute to the local alteration of the epithelial barrier of the respiratory tract, a hallmark of pertussis.


Subject(s)
Adenylate Cyclase Toxin/genetics , Bordetella pertussis/enzymology , Immunity, Innate/genetics , Whooping Cough/genetics , Adenylate Cyclase Toxin/metabolism , Bordetella pertussis/pathogenicity , Calmodulin/metabolism , Cell Membrane/metabolism , Cyclic AMP/genetics , Epithelial Cells/microbiology , Humans , Respiratory System/metabolism , Respiratory System/microbiology , Respiratory System/pathology , Whooping Cough/microbiology , Whooping Cough/pathology
3.
J Transl Med ; 18(1): 136, 2020 03 24.
Article in English | MEDLINE | ID: mdl-32209102

ABSTRACT

BACKGROUND: Chronic rhinosinusitis with nasal polyps (CRSwNP) is characterized by an alteration in airway epithelial cell functions including barrier function, wound repair mechanisms, mucociliary clearance. The mechanisms leading to epithelial cell dysfunction in nasal polyps (NPs) remain poorly understood. Our hypothesis was that among the inflammatory cytokines involved in NPs, IL-6 could alter epithelial repair mechanisms and mucociliary clearance. The aim of this study was to evaluate the in vitro effects of IL-6 on epithelial repair mechanisms in a wound repair model and on ciliary beating in primary cultures of Human Nasal Epithelial Cells (HNEC). METHODS: Primary cultures of HNEC taken from 38 patients during surgical procedures for CRSwNP were used in an in vitro model of wound healing. Effects of increasing concentrations of IL-6 (1 ng/mL, 10 ng/mL, and 100 ng/mL) and other ILs (IL-5, IL-9, IL-10) on wound closure kinetics were compared to cultures without IL-modulation. After wound closure, the differentiation process was characterized under basal conditions and after IL supplementation using cytokeratin-14, MUC5AC, and ßIV tubulin as immunomarkers of basal, mucus, and ciliated cells, respectively. The ciliated edges of primary cultures were analyzed on IL-6 modulation by digital high-speed video-microscopy to measure: ciliary beating frequency (CBF), ciliary length, relative ciliary density, metachronal wavelength and the ciliary beating efficiency index. RESULTS: Our results showed that: (i) IL-6 accelerated airway wound repair in vitro, with a dose-response effect whereas no effect was observed after other ILs-stimulation. After 24 h, 79% of wounded wells with IL6-100 were fully repaired, vs 46% in the IL6-10 group, 28% in the IL6-1 group and 15% in the control group; (ii) specific migration analyses of closed wound at late repair stage (Day 12) showed IL-6 had the highest migration compared with other ILs (iii) The study of the IL-6 effect on ciliary function showed that CBF and metachronal wave increased but without significant modifications of ciliary density, length of cilia and efficiency index. CONCLUSION: The up-regulated epithelial cell proliferation observed in polyps could be induced by IL-6 in the case of prior epithelial damage. IL-6 could be a major cytokine in NP physiopathology.


Subject(s)
Nasal Polyps , Rhinitis , Cells, Cultured , Chronic Disease , Epithelial Cells , Humans , Interleukin-6 , Nasal Mucosa , Nasal Polyps/pathology , Rhinitis/complications
4.
J Med Genet ; 57(4): 237-244, 2020 04.
Article in English | MEDLINE | ID: mdl-31772028

ABSTRACT

BACKGROUND: Primary ciliary dyskinesia (PCD) is a rare genetic disorder resulting in abnormal ciliary motility/structure, extremely heterogeneous at genetic and ultrastructural levels. We aimed, in light of extensive genotyping, to identify specific and quantitative ciliary beating anomalies, according to the ultrastructural phenotype. METHODS: We prospectively included 75 patients with PCD exhibiting the main five ultrastructural phenotypes (n=15/group), screened all corresponding PCD genes and measured quantitative beating parameters by high-speed video-microscopy (HSV). RESULTS: Sixty-eight (91%) patients carried biallelic mutations. Combined outer/inner dynein arms (ODA/IDA) defect induces total ciliary immotility, regardless of the gene involved. ODA defect induces a residual beating with dramatically low ciliary beat frequency (CBF) related to increased recovery stroke and pause durations, especially in case of DNAI1 mutations. IDA defect with microtubular disorganisation induces a low percentage of beating cilia with decreased beating angle and, in case of CCDC39 mutations, a relatively conserved mean CBF with a high maximal CBF. Central complex defect induces nearly normal beating parameters, regardless of the gene involved, and a gyrating motion in a minority of ciliated edges, especially in case of RSPH1 mutations. PCD with normal ultrastructure exhibits heterogeneous HSV values, but mostly an increased CBF with an extremely high maximal CBF. CONCLUSION: Quantitative HSV analysis in PCD objectives beating anomalies associated with specific ciliary ultrastructures and genotypes. It represents a promising approach to guide the molecular analyses towards the best candidate gene(s) to be analysed or to assess the pathogenicity of the numerous sequence variants identified by next-generation-sequencing.


Subject(s)
Axonemal Dyneins/genetics , Cilia/genetics , Ciliary Motility Disorders/genetics , Cytoskeletal Proteins/genetics , DNA-Binding Proteins/genetics , Adolescent , Adult , Axoneme/genetics , Axoneme/pathology , Child , Child, Preschool , Cilia/pathology , Ciliary Motility Disorders/diagnostic imaging , Ciliary Motility Disorders/pathology , Female , Genotype , High-Throughput Nucleotide Sequencing , Humans , Infant , Infant, Newborn , Male , Microscopy, Video , Middle Aged , Mutation/genetics , Phenotype , Young Adult
5.
PLoS Comput Biol ; 15(10): e1007408, 2019 10.
Article in English | MEDLINE | ID: mdl-31622332

ABSTRACT

Surfactant Replacement Therapy (SRT), which involves instillation of a liquid-surfactant mixture directly into the lung airway tree, is a major therapeutic treatment in neonatal patients with respiratory distress syndrome (RDS). This procedure has proved to be remarkably effective in premature newborns, inducing a five-fold decrease of mortality in the past 35 years. Disappointingly, its use in adults for treating acute respiratory distress syndrome (ARDS) experienced initial success followed by failures. Our recently developed numerical model has demonstrated that transition from success to failure of SRT in adults could, in fact, have a fluid mechanical origin that is potentially reversible. Here, we present the first numerical simulations of surfactant delivery into a realistic asymmetric conducting airway tree of the rat lung and compare them with experimental results. The roles of dose volume (VD), flow rate, and multiple aliquot delivery are investigated. We find that our simulations of surfactant delivery in rat lungs are in good agreement with our experimental data. In particular, we show that the monopodial architecture of the rat airway tree plays a major role in surfactant delivery, contributing to the poor homogeneity of the end distribution of surfactant. In addition, we observe that increasing VD increases the amount of surfactant delivered to the acini after losing a portion to coating the involved airways, the coating cost volume, VCC. Finally, we quantitatively assess the improvement resulting from a multiple aliquot delivery, a method sometimes employed clinically, and find that a much larger fraction of surfactant reaches the alveolar regions in this case. This is the first direct qualitative and quantitative comparison of our numerical model with experimental studies, which enhances our previous predictions in adults and neonates while providing a tool for predicting, engineering, and optimizing patient-specific surfactant delivery in complex situations.


Subject(s)
Pulmonary Surfactants/administration & dosage , Pulmonary Surfactants/therapeutic use , Animals , Computer Simulation , Hydrodynamics , Lung/physiology , Maximal Expiratory Flow Rate/physiology , Models, Anatomic , Models, Statistical , Rats , Rats, Long-Evans , Rats, Sprague-Dawley , Rats, Wistar , Surface-Active Agents
6.
Sci Rep ; 9(1): 12835, 2019 09 06.
Article in English | MEDLINE | ID: mdl-31492876

ABSTRACT

Enzymes speed up biochemical reactions at the core of life by as much as 15 orders of magnitude. Yet, despite considerable advances, the fine dynamical determinants at the microscopic level of their catalytic proficiency are still elusive. In this work, we use a powerful mathematical approach to show that rate-promoting vibrations in the picosecond range, specifically encoded in the 3D protein structure, are localized vibrations optimally coupled to the chemical reaction coordinates at the active site. Remarkably, our theory also exposes an hithertho unknown deep connection between the unique localization fingerprint and a distinct partition of the 3D fold into independent, foldspanning subdomains that govern long-range communication. The universality of these features is demonstrated on a pool of more than 900 enzyme structures, comprising a total of more than 10,000 experimentally annotated catalytic sites. Our theory provides a unified microscopic rationale for the subtle structure-dynamics-function link in proteins.


Subject(s)
Enzymes/chemistry , Vibration , Biocatalysis , Humans , L-Lactate Dehydrogenase/chemistry , Molecular Dynamics Simulation , Protein Conformation
7.
Biomech Model Mechanobiol ; 17(4): 961-973, 2018 Aug.
Article in English | MEDLINE | ID: mdl-29450740

ABSTRACT

During total liquid ventilation, lung cells are exposed to perfluorocarbon (PFC) whose chemophysical properties highly differ from standard aqueous cell feeding medium (DMEM). We herein perform a systematic study of structural and mechanical properties of A549 alveolar epithelial cells in order to characterize their response to PFC exposure, using DMEM as control condition. Changes in F-actin structure, focal adhesion density and glycocalyx distribution are evaluated by confocal fluorescent microscopy. Changes in cell mechanics and adhesion are measured by multiscale magnetic twisting cytometry (MTC). Two different microrheological models (single Voigt and power law) are used to analyze the cell mechanics characterized by cytoskeleton (CSK) stiffness and characteristic relaxation times. Cell-matrix adhesion is analyzed using a stochastic multibond deadhesion model taking into account the non-reversible character of the cell response, allowing us to quantify the adhesion weakness and the number of associated bonds. The roles of F-actin structure and glycocalyx layer are evaluated by depolymerizing F-actin and degrading glycocalyx, respectively. Results show that PFC exposure consistently induces F-actin remodeling, CSK softening and adhesion weakening. These results demonstrate that PFC triggers an alveolar epithelial cell response herein evidenced by a decay in intracellular CSK tension, an adhesion weakening and a glycocalyx layer redistribution. These PFC-induced cell adjustments are consistent with the hypothesis that cells respond to a decrease in adhesion energy at cell surface. This adhesion energy can be even further reduced in the presence of surfactant adsorbed at the cell surface.


Subject(s)
Alveolar Epithelial Cells/cytology , Alveolar Epithelial Cells/physiology , Fluorocarbons/pharmacology , A549 Cells , Actins/metabolism , Alveolar Epithelial Cells/drug effects , Biomechanical Phenomena , Cell Adhesion/drug effects , Cytochalasin D/pharmacology , Focal Adhesions/metabolism , Glycocalyx/metabolism , Humans , Polymerization , Polysaccharide-Lyases/metabolism , Surface-Active Agents/pharmacology
8.
Placenta ; 64 Suppl 1: S4-S8, 2018 04.
Article in English | MEDLINE | ID: mdl-29273272

ABSTRACT

Workshops are an important part of the IFPA annual meeting as they allow for discussion of specialized topics. At IFPA meeting 2017 there were four themed workshops, all of which are summarized in this report. These workshops discussed new knowledge and technological innovations in the following areas of research: 1) placental bed; 2) 3D structural modeling; 3) clinical placentology; 4) treatment of placental dysfunction.


Subject(s)
Models, Anatomic , Placenta Diseases/physiopathology , Placenta/physiology , Placentation/physiology , Female , Humans , Placenta/anatomy & histology , Placenta Diseases/pathology , Pregnancy
9.
PLoS Comput Biol ; 13(7): e1005552, 2017 Jul.
Article in English | MEDLINE | ID: mdl-28708866

ABSTRACT

Mucociliary clearance is one of the major lines of defense of the human respiratory system. The mucus layer coating the airways is constantly moved along and out of the lung by the activity of motile cilia, expelling at the same time particles trapped in it. The efficiency of the cilia motion can experimentally be assessed by measuring the velocity of micro-beads traveling through the fluid surrounding the cilia. Here we present a mathematical model of the fluid flow and of the micro-beads motion. The coordinated movement of the ciliated edge is represented as a continuous envelope imposing a periodic moving velocity boundary condition on the surrounding fluid. Vanishing velocity and vanishing shear stress boundary conditions are applied to the fluid at a finite distance above the ciliated edge. The flow field is expanded in powers of the amplitude of the individual cilium movement. It is found that the continuous component of the horizontal velocity at the ciliated edge generates a 2D fluid velocity field with a parabolic profile in the vertical direction, in agreement with the experimental measurements. Conversely, we show than this model can be used to extract microscopic properties of the cilia motion by extrapolating the micro-bead velocity measurement at the ciliated edge. Finally, we derive from these measurements a scalar index providing a direct assessment of the cilia beating efficiency. This index can easily be measured in patients without any modification of the current clinical procedures.


Subject(s)
Biological Clocks/physiology , Cilia/physiology , Lung/physiology , Models, Biological , Mucus/physiology , Respiratory Mucosa/physiology , Animals , Biological Transport, Active/physiology , Computer Simulation , Humans , Microfluidics/methods , Microspheres , Mucociliary Clearance/physiology
10.
PLoS Comput Biol ; 13(7): e1005605, 2017 Jul.
Article in English | MEDLINE | ID: mdl-28708889

ABSTRACT

Mucociliary clearance is one of the major lines of defense of the respiratory system. The mucus layer coating the pulmonary airways is moved along and out of the lung by the activity of motile cilia, thus expelling the particles trapped in it. Here we compare ex vivo measurements of a Newtonian flow induced by cilia beating (using micro-beads as tracers) and a mathematical model of this fluid flow, presented in greater detail in a second companion article. Samples of nasal epithelial cells placed in water are recorded by high-speed video-microscopy and ciliary beat pattern is inferred. Automatic tracking of micro-beads, used as markers of the flow generated by cilia motion, enables us also to assess the velocity profile as a function of the distance above the cilia. This profile is shown to be essentially parabolic. The obtained experimental data are used to feed a 2D mathematical and numerical model of the coupling between cilia, fluid, and micro-bead motion. From the model and the experimental measurements, the shear stress exerted by the cilia is deduced. Finally, this shear stress, which can easily be measured in the clinical setting, is proposed as a new index for characterizing the efficiency of ciliary beating.


Subject(s)
Biological Clocks/physiology , Cilia/physiology , Image Interpretation, Computer-Assisted/methods , Lung/physiology , Mucus/physiology , Respiratory Mucosa/physiology , Biological Transport, Active/physiology , Cilia/ultrastructure , Computer Simulation , Humans , Lung/cytology , Microfluidics/methods , Microscopy, Video/methods , Microspheres , Models, Biological , Mucociliary Clearance/physiology , Mucus/cytology
11.
Biol Cell ; 109(8): 293-311, 2017 Aug.
Article in English | MEDLINE | ID: mdl-28597954

ABSTRACT

BACKGROUND INFORMATION: The adenylate cyclase (CyaA) toxin is a major virulent factor of Bordetella pertussis, the causative agent of whooping cough. CyaA toxin is able to invade eukaryotic cells where it produces high levels of cyclic adenosine monophosphate (cAMP) affecting cellular physiology. Whether CyaA toxin can modulate cell matrix adhesion and mechanics of infected cells remains largely unknown. RESULTS: In this study, we use a recently proposed multiple bond force spectroscopy (MFS) with an atomic force microscope to assess the early phase of cell adhesion (maximal detachment and local rupture forces) and cell rigidity (Young's modulus) in alveolar epithelial cells (A549) for toxin exposure <1 h. At 30 min of exposure, CyaA toxin has a minimal effect on cell viability (>95%) at CyaA concentration of 0.5 nM, but a significant effect (≈81%) at 10 nM. MFS performed on A549 for three different concentrations (0.5, 5 and 10 nM) demonstrates that CyaA toxin significantly affects both cell adhesion (detachment forces are decreased) and cell mechanics (Young's modulus is increased). CyaA toxin (at 0.5 nM) assessed at three indentation/retraction speeds (2, 5 and 10 µm/s) significantly affects global detachment forces, local rupture events and Young modulus compared with control conditions, while an enzymatically inactive variant CyaAE5 has no effect. These results reveal the loading rate dependence of the multiple bonds newly formed between the cell and integrin-specific coated probe as well as the individual bond kinetics which are only slightly affected by the patho-physiological dose of CyaA toxin. Finally, theory of multiple bond force rupture enables us to deduce the bond number N which is reduced by a factor of 2 upon CyaA exposure (N ≈ 6 versus N ≈ 12 in control conditions). CONCLUSIONS: MFS measurements demonstrate that adhesion and mechanical properties of A549 are deeply affected by exposure to the CyaA toxin but not to an enzymatically inactive variant. This indicates that the alteration of cell mechanics triggered by CyaA is a consequence of the increase in intracellular cAMP in these target cells. SIGNIFICANCE: These results suggest that mechanical and adhesion properties of the cells appear as pertinent markers of cytotoxicity of CyaA toxin.


Subject(s)
Adenylate Cyclase Toxin/metabolism , Alveolar Epithelial Cells/physiology , Bordetella pertussis/enzymology , Bordetella pertussis/pathogenicity , Focal Adhesions/physiology , Integrins/metabolism , A549 Cells , Actin Cytoskeleton/metabolism , Alveolar Epithelial Cells/cytology , Alveolar Epithelial Cells/drug effects , Bordetella pertussis/drug effects , Cyclic AMP/metabolism , Focal Adhesions/drug effects , Humans , Whooping Cough/drug therapy , Whooping Cough/microbiology
12.
Biol Cell ; 109(7): 255-272, 2017 Jul.
Article in English | MEDLINE | ID: mdl-28543271

ABSTRACT

BACKGROUND INFORMATION: Integrin-mediated adhesion is a key process by which cells physically connect with their environment, and express sensitivity and adaptation through mechanotransduction. A critical step of cell adhesion is the formation of the first bonds which individually generate weak contacts (∼tens pN) but can sustain thousand times higher forces (∼tens nN) when associated. RESULTS: We propose an experimental validation by multiple bond force spectroscopy (MFS) of a stochastic model predicting adhesion reinforcement permitted by non-cooperative, multiple bonds on which force is homogeneously distributed (called parallel bond configuration). To do so, spherical probes (diameter: 6.6 µm), specifically coated by RGD-peptide to bind integrins, are used to statically indent and homogenously stretch the multiple bonds created for short contact times (2 s) between the bead and the surface of epithelial cells (A549). Using different separation speeds (v = 2, 5, 10 µm/s) and measuring cellular Young's modulus as well as the local stiffness preceding local rupture events, we obtain cell-by-cell the effective loading rates both at the global cell level and at the local level of individual constitutive bonds. Local rupture forces are in the range: f*=60-115 pN , whereas global rupture (detachment) forces reach F*=0.8-1.7 nN . Global and local rupture forces both exhibit linear dependencies with the effective loading rate, the slopes of these two linear relationships providing an estimate of the number of independent integrin bonds constituting the tested multiple bond structure (∼12). CONCLUSIONS: The MFS method enables to validate the reinforcement of integrin-mediated adhesion induced by the multiple bond configuration in which force is homogeneously distributed amongst parallel bonds. Local rupture events observed in the course of a spectroscopy manoeuver (MFS) lead to rupture force values considered in the literature as single-integrin bonds. SIGNIFICANCE: Adhesion reinforcement permitted by the parallel multiple bond association is particularly challenging to verify for two reasons: first, it is difficult to control precisely the direction of forces experimentally, and second, because both global and local bond rupture forces depend on the effective loading rate applied to the bond. Here, we propose an integrin-specific MFS method capable of detecting bond number and characterising bond configuration and its impact on adhesion strength.


Subject(s)
Alveolar Epithelial Cells/cytology , Cell Adhesion , Integrins/physiology , Mechanotransduction, Cellular , Microscopy, Atomic Force/methods , A549 Cells , Alveolar Epithelial Cells/physiology , Humans
14.
J Biomech Eng ; 138(12)2016 12 01.
Article in English | MEDLINE | ID: mdl-27551810

ABSTRACT

The mucociliary clearance in the bronchial tree is the main mechanism by which the lungs clear themselves of deposited particulate matter. In this work, a macroscopic model of the clearance mechanism is proposed. Lubrication theory is applied for thin films with both surface tension effects and a moving wall boundary. The flow field is computed by the use of a finite-volume scheme on an unstructured grid that replicates a bronchial bifurcation. The carina in bronchial bifurcations is of special interest because it is a location of increased deposition of inhaled particles. In this study, the mucus flow is computed for different values of the surface tension. It is found that a minimal surface tension is necessary for efficiently removing the mucus while maintaining the mucus film thickness at physiological levels.


Subject(s)
Bronchi/chemistry , Bronchi/physiopathology , Models, Biological , Models, Chemical , Mucociliary Clearance/physiology , Mucus/chemistry , Mucus/metabolism , Animals , Computer Simulation , Humans , Surface Tension
15.
Phys Rev Lett ; 117(7): 074301, 2016 Aug 12.
Article in English | MEDLINE | ID: mdl-27563967

ABSTRACT

A recent theoretical breakthrough has brought a new tool, called the localization landscape, for predicting the localization regions of vibration modes in complex or disordered systems. Here, we report on the first experiment which measures the localization landscape and demonstrates its predictive power. Holographic measurement of the static deformation under uniform load of a thin plate with complex geometry provides direct access to the landscape function. When put in vibration, this system shows modes precisely confined within the subregions delineated by the landscape function. Also the maxima of this function match the measured eigenfrequencies, while the minima of the valley network gives the frequencies at which modes become extended. This approach fully characterizes the low frequency spectrum of a complex structure from a single static measurement. It paves the way for controlling and engineering eigenmodes in any vibratory system, especially where a structural or microscopic description is not accessible.

16.
Biopolymers ; 105(7): 369-84, 2016 Jul.
Article in English | MEDLINE | ID: mdl-26900058

ABSTRACT

It is often envisioned that cations might coordinate at specific sites of nucleic acids and play an important structural role, for instance in the transition between B-DNA and Z-DNA. However, nucleic acid models explicitly devoid of specific sites may also exhibit features previously considered as evidence for specific binding. Such is the case of the "composite cylinder" (or CC) model which spreads out localized features of DNA structure and charge by cylindrical averaging, while sustaining the main difference between the B and Z structures, namely the better immersion of the B-DNA phosphodiester charges in the solution. Here, we analyze the non-electrostatic component of the free-energy difference between B-DNA and Z-DNA. We also compute the composition of the counterion sheath in a wide range of mixed-salt solutions and of temperatures: in contrast with the large difference of composition between the B-DNA and Z-DNA forms, the temperature dependence of sheath composition, previously unknown, is very weak. In order to validate the model, the mixed-salt predictions should be compared to experiment. We design a procedure for future measurements of the sheath composition based on Anomalous Small-Angle X-ray Scattering and complemented by (31) P NMR. With due consideration for the kinetics of the B-Z transition and for the capacity of generating at will the B or Z form in a single sample, the 5'-d[T-(m(5) C-G)12 -T] 26-mer emerges as a most suitable oligonucleotide for this study. Finally, the application of the finite element method to the resolution of the Poisson-Boltzmann equation is described in detail. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 369-384, 2016.


Subject(s)
DNA, B-Form/chemistry , DNA, Z-Form/chemistry , Oligonucleotides/chemistry , Kinetics , Magnetic Resonance Spectroscopy , Models, Molecular , Nucleic Acid Conformation , Salts/chemistry , Scattering, Small Angle , Solutions , Temperature , Thermodynamics , X-Ray Diffraction
17.
Phys Rev Lett ; 116(5): 056602, 2016 Feb 05.
Article in English | MEDLINE | ID: mdl-26894725

ABSTRACT

The amplitude of localized quantum states in random or disordered media may exhibit long-range exponential decay. We present here a theory that unveils the existence of an effective potential which finely governs the confinement of these states. In this picture, the boundaries of the localization subregions for low energy eigenfunctions correspond to the barriers of this effective potential, and the long-range exponential decay characteristic of Anderson localization is explained as the consequence of multiple tunneling in the dense network of barriers created by this effective potential. Finally, we show that Weyl's formula based on this potential turns out to be a remarkable approximation of the density of states for a large variety of one-dimensional systems, periodic or random.

18.
Biomech Model Mechanobiol ; 15(4): 947-63, 2016 08.
Article in English | MEDLINE | ID: mdl-26459324

ABSTRACT

Cellular adhesion forces depend on local biological conditions meaning that adhesion characterization must be performed while preserving cellular integrity. We presently postulate that magnetic bead twisting provides an appropriate stress, i.e., basically a clamp, for assessment in living cells of both cellular adhesion and mechanical properties of the cytoskeleton. A global dissociation rate obeying a Bell-type model was used to determine the natural dissociation rate ([Formula: see text]) and a reference stress ([Formula: see text]). These adhesion parameters were determined in parallel to the mechanical properties for a variety of biological conditions in which either adhesion or cytoskeleton was selectively weakened or strengthened by changing successively ligand concentration, actin polymerization level (by treating with cytochalasin D), level of exerted stress (by increasing magnetic torque), and cell environment (by using rigid and soft 3D matrices). On the whole, this multiscale evaluation of the cellular and molecular responses to a controlled stress reveals an evolution which is consistent with stochastic multiple bond theories and with literature results obtained with other molecular techniques. Present results confirm the validity of the proposed bead-twisting approach for its capability to probe cellular and molecular responses in a variety of biological conditions.


Subject(s)
Cytoskeleton/metabolism , Magnetics/methods , Microspheres , Models, Biological , A549 Cells , Cell Adhesion , Humans , Kinetics
19.
J Biomech ; 49(11): 2193-2200, 2016 07 26.
Article in English | MEDLINE | ID: mdl-26699945

ABSTRACT

Diffusional screening in the lungs is a physical phenomenon where the specific topological arrangement of alveolated airways of the respiratory region leads to a depletion, or 'screening', of oxygen molecules with increasing acinar generation. Here, we revisit diffusional screening phenomena in anatomically-inspired pulmonary acinar models under realistic breathing maneuvers. By modelling 3D bifurcating alveolated airways capturing both convection and diffusion, unsteady oxygen transport is investigated under cyclic breathing motion. To evaluate screening characteristics in the developing lungs during growth, four representative stages of lung development were chosen (i.e. 3 months, 1 year and 9 months, 3 years and adulthood) that capture distinct morphological acinar changes spanning alveolarization phases to isotropic alveolar growth. Numerical simulations unveil the dramatic changes in O2 transport occurring during lung development, where young infants exhibit highest acinar efficiencies that rapidly converge with age to predictions at adulthood. With increased ventilatory effort, transient dynamics of oxygen transport is fundamentally altered compared to tidal breathing and emphasizes the augmented role of convection. Resolving the complex convective acinar flow patterns in 3D acinar trees allows for the first time a spatially-localized and time-resolved characterization of oxygen transport in the pulmonary acinus, from infancy to adulthood.


Subject(s)
Lung/physiology , Models, Biological , Adult , Child, Preschool , Humans , Infant , Lung/anatomy & histology , Lung/growth & development , Movement , Respiration
20.
Biomicrofluidics ; 9(4): 044119, 2015 Jul.
Article in English | MEDLINE | ID: mdl-26392827

ABSTRACT

Fluid dynamics of mucus plug rupture is important to understand mucus clearance in lung airways and potential effects of mucus plug rupture on epithelial cells at lung airway walls. We established a microfluidic model to study mucus plug rupture in a collapsed airway of the 12th generation. Mucus plugs were simulated using Carbopol 940 (C940) gels at concentrations of 0.15%, 0.2%, 0.25%, and 0.3%, which have non-Newtonian properties close to healthy and diseased lung mucus. The airway was modeled with a polydimethylsiloxane microfluidic channel. Plug motion was driven by pressurized air. Global strain rates and shear stress were defined to quantitatively describe plug deformation and rupture. Results show that a plug needs to overcome yield stress before deformation and rupture. The plug takes relatively long time to yield at the high Bingham number. Plug length shortening is the more significant deformation than shearing at gel concentration higher than 0.15%. Although strain rates increase dramatically at rupture, the transient shear stress drops due to the shear-thinning effect of the C940 gels. Dimensionless time-averaged shear stress, T xy , linearly increases from 3.7 to 5.6 times the Bingham number as the Bingham number varies from 0.018 to 0.1. The dimensionless time-averaged shear rate simply equals to T xy /2. In dimension, shear stress magnitude is about one order lower than the pressure drop, and one order higher than yield stress. Mucus with high yield stress leads to high shear stress, and therefore would be more likely to cause epithelial cell damage. Crackling sounds produced with plug rupture might be more detectable for gels with higher concentration.

SELECTION OF CITATIONS
SEARCH DETAIL
...