Smeared multiscale finite element model for electrophysiology and ionic transport in biological tissue.

Basic functions of living organisms are governed by the nervous system through bidirectional signals transmitted from the brain to neural networks. These signals are similar to electrical waves. In electrophysiology the goal is to study the electrical properties of biological cells and tissues, and the transmission of signals. From a physics perspective, there exists a field of electrical potential within the living body, the nervous system, extracellular space and cells. Electrophysiological problems can be investigated experimentally and also theoretically by developing appropriate mathematical or computational models. Due to the enormous complexity of biological systems, it would be almost impossible to establish a detailed computational model of the electrical field, even for only a single organ (e.g. heart), including the entirety of cells comprising the neural network. In order to make computational models feasible for practical applications, we here introduce the concept of smeared fields, which represents a generalization of the previously formulated multiscale smeared methodology for mass transport in blood vessels, lymph, and tissue. We demonstrate the accuracy of the smeared finite element computational models for the electric field in numerical examples. The electrical field is further coupled with ionic mass transport within tissue composed of interstitial spaces extracellularly and by cytoplasm and organelles intracellularly. The proposed methodology, which couples electrophysiology and molecular ionic transport, is applicable to a variety of biological systems.

Correction function for accuracy improvement of the Composite Smeared Finite Element for diffusive transport in biological tissue systems.

Modeling of drug transport within capillaries and tissue remains a challenge, especially in tumors and cancers where the capillary network exhibits extremely irregular geometry. Recently introduced Composite Smeared Finite Element (CSFE) provides a new methodology of modeling complex convective and diffusive transport in the capillary-tissue system. The basic idea in the formulation of CSFE is in dividing the FE into capillary and tissue domain, coupled by 1D connectivity elements at each node. Mass transport in capillaries is smeared into continuous fields of pressure and concentration by introducing the corresponding Darcy and diffusion tensors. Despite theoretically correct foundation, there are still differences in the overall mass transport to (and from) tissue when comparing smeared model and a true 3D model. The differences arise from the fact that the smeared model cannot take into account the detailed non-uniform pressure and concentration distribution in the vicinity of capillaries. We introduced a field of correction function for diffusivity through the capillary walls of smeared models, in order to have the same mass accumulation in tissue as in case of true 3D models. The parameters of the numerically determined correction function are: ratio of thickness and diameter of capillary wall, ratio of diffusion coefficient in capillary wall and surrounding tissue; and volume fraction of capillaries within tissue domain. Partitioning at the capillary wall - blood interface can also be included. It was shown that the correction function is applicable to complex configurations of capillary networks, providing improved accuracy of our robust smeared models in computer simulations of real transport problems, such as in tumors or human organs.

Progression-dependent transport heterogeneity of breast cancer liver metastases as a factor in therapeutic resistance.

Metastatic disease is a major cause of mortality in cancer patients. While many drug delivery strategies for anticancer therapeutics have been developed in preclinical studies of primary tumors, the drug delivery properties of metastatic tumors have not been sufficiently investigated. Therapeutic efficacy hinges on efficient drug permeation into the tumor microenvironment, which is known to be heterogeneous thus potentially making drug permeation heterogeneous, also. In this study, we have identified that 4 T1 liver metastases, treated with pegylated liposomal doxorubicin, have unfavorable and heterogeneous transport of doxorubicin. Our drug extravasation results differ greatly from analogous studies with 4 T1 tumors growing in the primary site. A probabilistic tumor population model was developed to estimate drug permeation efficiency and drug kinetics of liver metastases by integrating the transport and structural properties of tumors and delivered drugs. The results demonstrate significant heterogeneity in metastases with regard to transport properties of doxorubicin within the same animal model, and even within the same organ. These results also suggest that the degree of heterogeneity depends on the stage of tumor progression and that differences in transport properties can define transport-based tumor phenotypes. These findings may have valuable clinical implications by illustrating that therapeutic agents can permeate and eliminate metastases of "less resistant" transport phenotypes, while sparing tumors with more "resistant" transport properties. We anticipate that these results could challenge the current paradigm of drug delivery into metastases, highlight potential caveats for therapies that may alter tumor perfusion, and deepen our understanding of the emergence of drug transport-based therapeutic resistance.

Multiscale smeared finite element model for mass transport in biological tissue: From blood vessels to cells and cellular organelles.

One of the basic and vital processes in living organisms is mass exchange, which occurs on several levels: it goes from blood vessels to cells and organelles within cells. On that path, molecules, as oxygen, metabolic products, drugs, etc. Traverse different macro and micro environments - blood, extracellular/intracellular space, and interior of organelles; and also biological barriers such as walls of blood vessels and membranes of cells and organelles. Many aspects of this mass transport remain unknown, particularly the biophysical mechanisms governing drug delivery. The main research approach relies on laboratory and clinical investigations. In parallel, considerable efforts have been directed to develop computational tools for additional insight into the intricate process of mass exchange and transport. Along these lines, we have recently formulated a composite smeared finite element (CSFE) which is composed of the smeared continuum pressure and concentration fields of the capillary and lymphatic system, and of these fields within tissue. The element offers an elegant and simple procedure which opens up new lines of inquiry and can be applied to large systems such as organs and tumors models. Here, we extend this concept to a multiscale scheme which concurrently couples domains that span from large blood vessels, capillaries and lymph, to cell cytosol and further to organelles of nanometer size. These spatial physical domains are coupled by the appropriate connectivity elements representing biological barriers. The composite finite element has "degrees of freedom" which include pressures and concentrations of all compartments of the vessels-tissue assemblage. The overall model uses the standard, measurable material properties of the continuum biological environments and biological barriers. It can be considered as a framework into which we can incorporate various additional effects (such as electrical or biochemical) for transport through membranes or within cells. This concept and the developed FE software within our package PAK offers a computational tool that can be applied to whole-organ systems, while also including specific domains such as tumors. The solved examples demonstrate the accuracy of this model and its applicability to large biological systems.

Mass release curves as the constitutive curves for modeling diffusive transport within biological tissue.

In diffusion governed by Fick's law, the diffusion coefficient represents the phenomenological material parameter and is, in general, a constant. In certain cases of diffusion through porous media, the diffusion coefficient can be variable (i.e. non-constant) due to the complex process of solute displacements within microstructure, since these displacements depend on porosity, internal microstructural geometry, size of the transported particles, chemical nature, and physical interactions between the diffusing substance and the microstructural surroundings. In order to provide a simple and general approach of determining the diffusion coefficient for diffusion through porous media, we have introduced mass release curves as the constitutive curves of diffusion. The mass release curve for a selected direction represents cumulative mass (per surface area) passed in that direction through a small reference volume, in terms of time. We have developed a methodology, based on numerical Finite Element (FE) and Molecular Dynamics (MD) methods, to determine simple mass release curves of solutes through complex media from which we calculate the diffusion coefficient. The diffusion models take into account interactions between solute particles and microstructural surfaces, as well as hydrophobicity (partitioning). We illustrate the effectiveness of our approach on several examples of complex composite media, including an imaging-based analysis of diffusion through pancreatic cancer tissue. The presented work offers an insight into the role of mass release curves in describing diffusion through porous media in general, and further in case of complex composite media such as biological tissue.

A composite smeared finite element for mass transport in capillary systems and biological tissue.

One of the key processes in living organisms is mass transport occurring from blood vessels to tissues for supplying tissues with oxygen, nutrients, drugs, immune cells, and - in the reverse direction - transport of waste products of cell metabolism to blood vessels. The mass exchange from blood vessels to tissue and vice versa occurs through blood vessel walls. This vital process has been investigated experimentally over centuries, and also in the last decades by the use of computational methods. Due to geometrical and functional complexity and heterogeneity of capillary systems, it is however not feasible to model in silico individual capillaries (including transport through the walls and coupling to tissue) within whole organ models. Hence, there is a need for simplified and robust computational models that address mass transport in capillary-tissue systems. We here introduce a smeared modeling concept for gradient-driven mass transport and formulate a new composite smeared finite element (CSFE). The transport from capillary system is first smeared to continuous mass sources within tissue, under the assumption of uniform concentration within capillaries. Here, the fundamental relation between capillary surface area and volumetric fraction is derived as the basis for modeling transport through capillary walls. Further, we formulate the CSFE which relies on the transformation of the one-dimensional (1D) constitutive relations (for transport within capillaries) into the continuum form expressed by Darcy's and diffusion tensors. The introduced CSFE is composed of two volumetric parts - capillary and tissue domains, and has four nodal degrees of freedom (DOF): pressure and concentration for each of the two domains. The domains are coupled by connectivity elements at each node. The fictitious connectivity elements take into account the surface area of capillary walls which belongs to each node, as well as the wall material properties (permeability and partitioning). The overall FE model contains geometrical and material characteristics of the entire capillary-tissue system, with physiologically measurable parameters assigned to each FE node within the model. The smeared concept is implemented into our implicit-iterative FE scheme and into FE package PAK. The first three examples illustrate accuracy of the CSFE element, while the liver and pancreas models demonstrate robustness of the introduced methodology and its applicability to real physiological conditions.

Burkholderia cepacia complex in Serbian patients with cystic fibrosis: prevalence and molecular epidemiology.

The Burkholderia cepacia complex (Bcc) organisms remain significant pathogens in patients with cystic fibrosis (CF). This study was performed to evaluate the prevalence, epidemiological characteristics, and presence of molecular markers associated with virulence and transmissibility of the Bcc strains in the National CF Centre in Belgrade, Serbia. The Bcc isolates collected during the four-year study period (2010-2013) were further examined by 16 s rRNA gene, pulsed-field gel electrophoresis of genomic DNA, multilocus sequence typing analysis, and phylogenetic analysis based on concatenated sequence of seven alleles. Fifty out of 184 patients (27.2 %) were colonized with two Bcc species, B. cenocepacia (n = 49) and B. stabilis (n = 1). Thirty-four patients (18.5 %) had chronic colonization. Typing methods revealed a high level of similarity among Bcc isolates, indicating a person-to-person transmission or acquisition from a common source. New sequence types (STs) were identified, and none of the STs with an international distribution were found. One centre-specific ST, B. cenocepacia ST856, was highly dominant and shared by 48/50 (96 %) patients colonized by Bcc. This clone was characterized by PCR positivity for both the B. cepacia epidemic strain marker and cable pilin, and showed close genetic relatedness to the epidemic strain CZ1 (ST32). These results indicate that the impact of Bcc on airway colonization in the Serbian CF population is high and virtually exclusively limited to a single clone of B. cenocepacia. The presence of a highly transmissible clone and probable patient-to-patient spread was observed.

Gut-associated lymphoid tissue, gut microbes and susceptibility to experimental autoimmune encephalomyelitis.

Gut microbiota and gut-associated lymphoid tissue have been increasingly appreciated as important players in pathogenesis of various autoimmune diseases, including multiple sclerosis. Experimental autoimmune encephalomyelitis (EAE) is an animal model of multiple sclerosis that can be induced with an injection of spinal cord homogenate emulsified in complete Freund's adjuvant in Dark Agouti (DA) rats, but not in Albino Oxford (AO) rats. In this study, mesenteric lymph nodes (MLN), Peyer's patches (PP) and gut microbiota were analysed in these two rat strains. There was higher proportion of CD4(+) T cells and regulatory T cells in non-immunised DA rats in comparison to AO rats. Also, DA rat MLN and PP cells were higher producers of pro-inflammatory cytokines interferon-γ and interleukin-17. Finally, microbial analyses showed that uncultivated species of Turicibacter and Atopostipes genus were exclusively present in AO rats, in faeces and intestinal tissue, respectively. Thus, it is clear that in comparison of an EAE-susceptible with an EAE-resistant strain of rats, various discrepancies at the level of gut associated lymphoid tissue, as well as at the level of gut microbiota can be observed. Future studies should determine if the differences have functional significance for EAE pathogenesis.

A multiscale MD-FE model of diffusion in composite media with internal surface interaction based on numerical homogenization procedure.

Mass transport by diffusion within composite materials may depend not only on internal microstructural geometry, but also on the chemical interactions between the transported substance and the material of the microstructure. Retrospectively, there is a gap in methods and theory to connect material microstructure properties with macroscale continuum diffusion characteristics. Here we present a new hierarchical multiscale model for diffusion within composite materials that couples material microstructural geometry and interactions between diffusing particles and the material matrix. This model, which bridges molecular dynamics (MD) and the finite element (FE) method, is employed to construct a continuum diffusion model based on a novel numerical homogenization procedure. The procedure is general and robust for evaluating constitutive material parameters of the continuum model. These parameters include the traditional bulk diffusion coefficients and, additionally, the distances from the solid surface accounting for surface interaction effects. We implemented our models to glucose diffusion through the following two geometrical/material configurations: tightly packed silica nanospheres, and a complex fibrous structure surrounding nanospheres. Then, rhodamine 6G diffusion analysis through an aga-rose gel network was performed, followed by a model validation using our experimental results. The microstructural model, numerical homogenization and continuum model offer a new platform for modeling and predicting mass diffusion through complex biological environment and within composite materials that are used in a wide range of applications, like drug delivery and nanoporous catalysts.

Novel antilisterial bacteriocin licheniocin 50.2 from Bacillus licheniformis VPS50.2 isolated from soil sample.

AIM: To isolate and characterize bacteriocin, licheniocin 50.2, from soil bacteria identified as Bacillus licheniformis. METHODS AND RESULTS: The strain B. licheniformis VPS50.2 was identified as bacteriocin producer, effective against Gram-positive bacteria, including Listeria monocytogenes, methicillin-resistant Staphylococcus aureus (MRSA) and ß-haemolytic streptococci. The start of bacteriocin production coincides with the beginning of sporulation. Ammonium sulfate precipitation, chloroform extraction and ultrafiltration were used for bacteriocin purification. MALDI TOF/TOF mass spectrometry of purified sample detected the protein with molecular mass of 3253·209 Da. N-terminal sequencing recognized first 15 amino acids with the sequence: W E E Y N I I X Q L G N K G Q. We named the newly characterized bacteriocin as subclass II.3 bacteriocin, licheniocin 50·2. The bacteriocin activity was insensitive to lysozyme and proteinase K, heat stable after incubation at 100°C for 30 min and over wide range of pH (2-12). MICs of crude bacteriocin extract were determined for L. monocytogenes and MRSA. Time-kill study showed that licheniocin had bactericidal effect to L. monocytogenes. CONCLUSION: A novel, thermostable, pH-tolerant bacteriocin active against Gram-positive bacteria was isolated. SIGNIFICANCE AND IMPACT OF THE STUDY: Attributes of new, stable licheniocin 50.2 make it a promising agent for application as biopreservative in food industry.

Interfacial effects on nanoconfined diffusive mass transport regimes.

A hierarchical multiscale modeling approach, incorporating molecular dynamics and finite element techniques, is used to study parametrically diffusion regimes through nanoconfined fluid. Novel parameters that determine the character of the diffusion regime and diffusion kinetics within the nanoscale confined fluids is established by exploring diffusion where the interface effects at the solid surface are important. New diffusion transport characteristics are established when nanochannel confining dimension approaches 3-4 sizes of diffusing molecules, which also marks peripheries of the non-fickian transport regime.

Geometric hysteresis of alveolated ductal architecture.

Low Reynolds number airflow in the pulmonary acinus and aerosol particle kinetics therein are significantly conditioned by the nature of the tidal motion of alveolar duct geometry. At least two components of the ductal structure are known to exhibit stress-strain hysteresis: smooth muscle within the alveolar entrance rings, and surfactant at the air-tissue interface. We hypothesize that the geometric hysteresis of the alveolar duct is largely determined by the interaction of the amount of smooth muscle and connective tissue in ductal rings, septal tissue properties, and surface tension-surface area characteristics of surfactant. To test this hypothesis, we have extended the well-known structural model of the alveolar duct by Wilson and Bachofen (1982, "A Model for Mechanical Structure of the Alveolar Duct," J. Appl. Physiol. 52(4), pp. 1064-1070) by adding realistic elastic and hysteretic properties of (1) the alveolar entrance ring, (2) septal tissue, and (3) surfactant. With realistic values for tissue and surface properties, we conclude that: (1) there is a significant, and underappreciated, amount of geometric hysteresis in alveolar ductal architecture; and (2) the contribution of smooth muscle and surfactant to geometric hysteresis are of opposite senses, tending toward cancellation. Quantitatively, the geometric hysteresis found experimentally by Miki et al. (1993, "Geometric Hysteresis in Pulmonary Surface-to-Volume Ratio during Tidal Breathing," J. Appl. Physiol. 75(4), pp. 1630-1636) is consistent with little or no smooth muscle tone in anesthetized rabbits in control conditions, and with substantial smooth muscle activation following methacholine challenge. The observed local hysteretic boundary motion of the acinar duct would result in irreversible acinar flow fields, which might be important mechanistic contributors to aerosol mixing and deposition deep in the lung.

Particle-induced indentation of the alveolar epithelium caused by surface tension forces.

Physical contact between an inhaled particle and alveolar epithelium at the moment of particle deposition must have substantial effects on subsequent cellular functions of neighboring cells, such as alveolar type-I, type-II pneumocytes, alveolar macrophage, as well as afferent sensory nerve cells, extending their dendrites toward the alveolar septal surface. The forces driving this physical insult are born at the surface of the alveolar air-liquid layer. The role of alveolar surfactant submerging a hydrophilic particle has been suggested by Gehr and Schürch's group (e.g., Respir Physiol 80: 17-32, 1990). In this paper, we extended their studies by developing a further comprehensive and mechanistic analysis. The analysis reveals that the mechanics operating in the particle-tissue interaction phenomena can be explained on the basis of a balance between surface tension force and tissue resistance force; the former tend to move a particle toward alveolar epithelial cell surface, the latter to resist the cell deformation. As a result, the submerged particle deforms the tissue and makes a noticeable indentation, which creates unphysiological stress and strain fields in tissue around the particle. This particle-induced microdeformation could likely trigger adverse mechanotransduction and mechanosensing pathways, as well as potentially enhancing particle uptake by the cells.

Regulation of the sdsA alkyl sulfatase of Pseudomonas sp. ATCC19151 and its involvement in degradation of anionic surfactants.

AIMS: The presented study was aimed to reveal transcriptional regulation of genes involved in SDS degradation (sdsA and sdsB) in Pseudomonas sp. ATCC19151. In addition, the ability of Pseudomonas sp. ATCC19151 to degrade anionic surfactants present in commercial detergent and septic tank drain was analysed. METHODS AND RESULTS: Strain ATCC19151, at 30°C, degrades all SDS present in the liquid medium (up to 4% w/v of SDS) within 48 h. ATCC19151 grows in the presence up to 15% (v/v) 'Fairy' commercial detergent and mineralizes 35% of present anionic surfactants. Analysis of the sdsA (P(sdsA) ) and divergent sdsB (P(sdsB) ) gene promoter activities revealed that SdsB acts as a positive regulator of sdsA and sdsB transcription. P(sdsA) and P(sdsB) activities rose significantly in the presence of the SDS, indicating inducibility of sdsA and sdsB transcription. DNA-binding assay indicated that SdsB directly regulates the transcription of sdsA and sdsB genes. Strain ATCC19151 grew in a sterile septic tank drain and on commercial detergent as sole source of carbon. CONCLUSIONS: SdsA enables Pseudomonas sp. ATCC19151 to utilize SDS as a sole carbon source. SdsB is positive transcriptional regulator of sdsA and sdsB genes. SIGNIFICANCE AND IMPACT OF THE STUDY: Ability of ATCC19151 to degrade anionic surfactants makes Pseudomonas sp. ATCC19151 a good candidate for bioremediation.

The presence of prtP proteinase gene in natural isolate Lactobacillus plantarum BGSJ3-18.

AIMS: The study of proteolytic activity and examination of proteinase gene region organization in proteolytically active Lactobacillus plantarum strains from different natural sources. METHODS AND RESULTS: A set of 37 lactobacilli was distinguished by using multiplex PCR assay. Results showed that 34 strains were Lact. plantarum and three of them were Lact. paraplantarum. The examination of proteolytic activity revealed that 28 Lact. plantarum and two Lact. paraplantarum hydrolyse beta-casein. Further analyses of all proteolytically active Lact. plantarum with primers specific for different types of CEPs demonstrated that strain BGSJ3-18 has prtP catalytic domain as well as prtP-prtM intergenic region showing more than 95% sequence identity with the same regions present in Lact. paracasei, Lact. casei and L. lactis. No presence of prtB, prtH or prtR proteinase genes was detected in any of tested Lact. plantarum strains. CONCLUSIONS: One out of 28 analysed Lact. plantarum strains harbours the prtP-like gene. The other proteolytically active Lact. plantarum probably possesses a different type of extracellular proteinase(s). SIGNIFICANCE AND IMPACT OF THE STUDY: It is the first report about the presence of the prtP-like gene in Lact. plantarum, which illustrates the mobility of this gene and its presence in different species.

Molecular characterization of plasmids pS7a and pS7b from Lactococcus lactis subsp. lactis bv. diacetylactis S50 as a base for the construction of mobilizable cloning vectors.

AIMS: Strain Lactococcus lactis subsp. lactis bv. diacetylactis S50 harbours five theta-replicating plasmids (pS6, pS7a, pS7b, pS80 and pS140). The aim of this study was to characterize domains involved in the replication and conjugative mobilization of the small plasmids pS7a and pS7b, which are structurally very similar. METHODS AND RESULTS: Complete nucleotide sequences of pS7a and pS7b were determined by cloning DNA fragments of different sizes into Escherichia coli vectors. Linearized plasmids and four EcoRI fragments of the pS7a and pS7b were cloned into an origin probe vector. Constructed plasmids (pSEV10, pSK10, pISE1a and pISE1b) were able to replicate in the strain L. lactis subsp. cremoris MG1363. In addition, experiments showed that plasmids pS7a and pS7b contained oriT sequences and their conjugative transfer directly depended on the presence of pS80 in donor cells. CONCLUSIONS: Plasmids pS7a and pS7b contained typical lactococcal theta replication origin and repB gene that enable them to replicate in the strain L. lactis subsp. cremoris MG1363. Plasmid pS80 plays a key role in the conjugative transfer of small plasmids. SIGNIFICANCE AND IMPACT OF THE STUDY: Plasmids pS7a and pS7b-based derivatives could be valuable tools for genetic manipulation, studying processes of plasmid maintenance and horizontal gene transfer in lactococci.

Modelling thrombosis using dissipative particle dynamics method.

AIM: Arterial occlusion is a leading cause of cardiovascular disease. The main mechanism causing vessel occlusion is thrombus formation, which may be initiated by the activation of platelets. The focus of this study is on the mechanical aspects of platelet-mediated thrombosis which includes the motion, collision, adhesion and aggregation of activated platelets in the blood. A review of the existing continuum-based models is given. A mechanical model of platelet accumulation onto the vessel wall is developed using the dissipative particle dynamics (DPD) method in which the blood (i.e. colloidal-composed medium) is treated as a group of mesoscale particles interacting through conservative, dissipative, attractive and random forces. METHODS: Colloidal fluid components (plasma and platelets) are discretized by mesoscopic (micrometre-size) particles that move according to Newton's law. The size of each mesoscopic particle is small enough to allow tracking of each constituent of the colloidal fluid, but significantly larger than the size of atoms such that, in contrast to the molecular dynamics approach, detailed atomic level analysis is not required. RESULTS: To test this model, we simulated the deposition of platelets onto the wall of an expanded tube and compared our computed results with the experimental data of Karino et al. (Miscrovasc. Res. 17, 238-269, 1977). By matching our simulations to the experimental results, the platelet aggregation/adhesion binding force (characterized by an effective spring constant) was determined and found to be within a physiologically reasonable range. CONCLUSION: Our results suggest that the DPD method offers a promising new approach to the modelling of platelet-mediated thrombosis. The DPD model includes interaction forces between platelets both when they are in the resting state (non-activated) and when they are activated, and therefore it can be extended to the analysis of kinetics of binding and other phenomena relevant to thrombosis.

Purification of bacteriocin LS1 produced by human oral isolate Lactobacillus salivarius BGHO1.

INTRODUCTION: Lactobacillus salivarius BGHO1, a human oral isolate with antagonistic activity against growth of Streptococcus mutans, Streptococcus pneumoniae, Staphylococcus aureus, Enterococcus faecalis, Micrococcus flavus, and Salmonella enteritidis, probably produces more than one proteinaceous antimicrobial substance. The objective of this study was the purification of a bacteriocin, named LS1, produced by L. salivarius BGHO1. METHODS: A simple and fast procedure for bacteriocin purification was developed, consisting of reverse-phase chromatography of the ammonium sulfate precipitate of cell-free culture supernatant by fast protein liquid chromatography and high-performance liquid chromatography, followed by tricine sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), with the subsequent extraction of bacteriocin from the gel. RESULTS: The supernatant of L. salivarius BGHO1 culture retained its antimicrobial activity after boiling in a water bath for 15 min. Its antimicrobial activity was also maintained even after treatment for 20 min at 121 degrees C in an autoclave. Bacteriocin LS1 was purified to homogeneity. The molecular mass of bacteriocin LS1 was estimated to be approximately 10 kDa, based on tricine SDS-PAGE. During purification, another compound with antimicrobial activity, produced by L. salivarius BGHO1, was detected. The molecular mass of this compound was estimated to be approximately 5 kDa, based on tricine SDS-PAGE. CONCLUSION: Our results imply that LS1 is most probably a new bacteriocin, different from previously described bacteriocins produced by L. salivarius strains. The purification of bacteriocin LS1 enabled the further characterization of LS1 on both the molecular and genetic levels.

Interactions of blood cell constituents: experimental investigation and computational modeling by discrete particle dynamics algorithm.

When the size of individual blood constituents [e.g., red blood cells (RBCs), white blood cells, platelets] becomes comparable to the size of blood vessels, the interactions among blood constituents in determining the blood behavior can no longer be ignored. In this paper, we have developed a comprehensive computational model to simulate the motion of an individual platelet in the plasma medium and its binding to the microvessel wall. The model is based on a Discrete Particle Dynamics (DPD) algorithm, in which blood plasma, platelets and the vessel walls are treated as a group of discretized mesoscopic size particles interacting through conservative, dissipative and random forces. Deposition (i.e., binding) of platelets is modeled by considering attractive forces at the vessel wall, which is characterized by the values of the effective spring constant for platelet adhesion. To test this model, we simulated platelet deposition in a perfusion chamber. By matching the simulation results to experimental data, the effective platelet spring constants were determined and were found to be approximately 50 N/m, which is within a physiologically relevant range. It is demonstrated that the DPD analysis offers the capability of simulating the time-dependent binding of platelets. We conclude that this model provides a new approach for studying the interaction among blood constituents.

Dissipative particle dynamics simulation of flow generated by two rotating concentric cylinders: boundary conditions.

The dissipative particle dynamics (DPD) method was used to simulate the flow in a system comprised of a fluid occupying the space between two cylinders rotating with equal angular velocities. The fluid, initially at rest, ultimately reaches a steady, linear velocity distribution (a rigid-body rotation). Since the induced flow field is solely associated with the no-slip boundary condition at the walls, we employed this system as a benchmark to examine the effect of bounce-back reflections, specular reflections, and Pivkin-Karniadakis no-slip boundary conditions, upon the steady-state velocity, density, and temperature distributions. An additional advantage of the foregoing system is that the fluid occupies inherently a finite bounded domain so that the results are affected by the prescribed no-slip boundary conditions only. Past benchmark systems such as Couette flow between two infinite parallel plates or Poiseuille flow in an infinitely long cylinder must employ artificial periodic boundary conditions at arbitrary upstream and downstream locations, a possible source of spurious effects. In addition, the effect of the foregoing boundary conditions on the time evolution of the simulated velocity profile was compared with that of the known, time-dependent analytical solution. It was shown that bounce-back reflection yields the best results for the velocity distributions with small fluctuations in density and temperature at the inner fluid domain and larger deviations near the walls. For the unsteady solutions a good fit is obtained if the DPD friction coefficient is proportional to the kinematic viscosity. Based on dimensional analysis and the numerical results a universal correlation is suggested between the friction coefficient and the kinematic viscosity.