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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Modeling of muscle fatigue using Hill's model

A new model incorporating muscle fatigue has been developed to predict the effect of muscle fatigue on the force-time relationship of skeletal muscle by using the PAK-program. Differential equations in the incremental form have been implemented into Hill's muscle model. In order to describe the effect of muscle fatigue and recovery on skeletal muscle behaviors, a set of equations in terms of three phenomenological parameters which are a fatigue curve under sustained maximal activation, a recovery curve and an endurance function were developed. With reference to existing models and experimental results, the input parameters for fatigue curve under sustained maximal activation and endurance function were determined. The model has been investigated under an isometric condition. The effects of different shapes of the recovery curves have also been considered in this model. Validation of the model has been performed by comparing the predicted results with the experimental data from an existing literature.

Regulation of rpoS gene expression in Pseudomonas: involvement of a TetR family regulator

The rpoS gene encodes the sigma factor which was identified in several gram-negative bacteria as a central regulator during stationary phase. rpoS gene regulation is known to respond to cell density, showing higher expression in stationary phase. For Pseudomonas aeruginosa, it has been demonstrated that the cell-density-dependent regulation response known as quorum sensing interacts with this regulatory response. Using the rpoS promoter of P. putida, we identified a genomic Tn5 insertion mutant of P. putida which showed a 90% decrease in rpoS promoter activity, resulting in less RpoS being present in a cell at stationary phase. Molecular analysis revealed that this mutant carried a Tn5 insertion in a gene, designated psrA (Pseudomonas sigma regulator), which codes for a protein (PsrA) of 26.3 kDa. PsrA contains a helix-turn-helix motif typical of DNA binding proteins and belongs to the TetR family of bacterial regulators. The homolog of the psrA gene was identified in P. aeruginosa; the protein showed 90% identity to PsrA of P. putida. A psrA::Tn5 insertion mutant of P. aeruginosa was constructed. In both Pseudomonas species, psrA was genetically linked to the SOS lexA repressor gene. Similar to what was observed for P. putida, a psrA null mutant of P. aeruginosa also showed a 90% reduction in rpoS promoter activity; both mutants could be complemented for rpoS promoter activity when the psrA gene was provided in trans. psrA mutants of both Pseudomonas species lost the ability to induce rpoS expression at stationary phase, but they retained the ability to produce quorum-sensing autoinducer molecules. PsrA was demonstrated to negatively regulate psrA gene expression in Pseudomonas and in Escherichia coli as well as to be capable of activating the rpoS promoter in E. coli. Our data suggest that PsrA is an important regulatory protein of Pseudomonas spp. involved in the regulatory cascade controlling rpoS gene regulation in response to cell density.

Disruptions of the Ustilago maydis REC2 gene identify a protein domain important in directing recombinational repair of DNA

The REC2 gene of Ustilago maydis encodes a homologue of the Escherichia coli RecA protein and was first identified in a screen for UV-sensitive mutants. The original isolate, rec2-1, was found to be deficient in repair of DNA damage, genetic recombination and meiosis. We report here that the rec2-197 allele, which was constructed by gene disruption, retains some biological activity and is partially dominant with respect to REC2. The basis for the residual activity is probably as a result of expression of a diffusible product from the rec2-197 allele that augments or interferes with REC2 functions. This product appears to be a polypeptide expressed from a remnant of the 5' end of the open reading frame that was not removed in creating the gene disruption. The mutator activity and disturbed meiosis of rec2-197 suggest that the Rec2 protein functions in a process that avoids spontaneous mutation and insures faithful meiotic chromosome segregation. A prediction based on the phenotype of rec2-197 is that Rec2 protein interacts with one or more other proteins in directing these functions. To identify interacting proteins we performed a yeast two-hybrid screen and found Rad51 as a candidate. Rec2-197 and Rad51 appear to interact to a similar degree.

Characterization of cell envelope-associated proteinases of thermophilic lactobacilli

The proteolytic activities of two natural isolates of thermophilic lactobacilli, Lactobacillus acidophilus BGRA43 and Lact. delbrueckii BGPF1, and Lact. acidophilus CH2 (Chr. Hansen's strain) and Lact. acidophilus V74 (Visby's strain), were compared. Results revealed that optimal pH for all four proteinases is 6.5, whereas temperature optimum varied among proteinases. Determination of caseinolytic activity done under optimal conditions for each strain revealed that the CH2 and V74 proteinases completely hydrolysed both alphaS1-casein and beta-casein, showing very low activity towards kappa-casein. The BGPF1 proteinase completely hydrolysed only beta-casein. The BGRA43 proteinase completely hydrolysed all three casein fractions. The proteolytic activities of whole cells were inhibited by serine proteinase inhibitors, suggesting that all four strains produce serine proteinases. DNA-DNA hybridization and PCR analysis showed that BGPF1 contains the prtB-like proteinase gene. Characterized thermophilic strains BGPF1 and BGRA43 were successfully used as starter cultures for production of yoghurt and acidophilus milk, respectively.

Shuttle vectors for genetic manipulations in Ustilago maydis

Shuttle vectors with new or improved features were constructed to enable facile genetic manipulations in the plant pathogen Ustilago maydis. Sets of plasmids selectable in media containing geneticin, carboxin, nourseothricin, or hygromycin, able to replicate autonomously, to transform U. maydis by integration, and to express foreign genes under control of the homologous glyceraldehyde-3-phosphate dehydrogenase promoter, were built upon a common pUC19 vector backbone. This permits a large number of choices for a cloning site, blue/white screening for recombinant plasmids, rapid transfer of a cloned DNA fragment between plasmids, and choice of several dominant drug-resistance markers for selection in U. maydis.

Gentamicin-resistance determinants confer background-dependent hygromycin B resistance

Micromonospora strains that produce aminoglycoside antibiotics have a high level of resistance to their own products and to structurally similar antibiotics with a 4,6-disubstituted deoxystreptamine aminocyclitol component such as neomycin, kanamycin, or gentamicin, but these strains remain susceptible to other aminoglycosides such as neomycin and apramycin, in which the aminocyclitol component has different types of substitutions. Therefore, it was surprising that the aminoglycoside-producing Micromonospora strains examined here also showed high-level resistance to hygromycin B, in spite of the fact that this compound has a structurally different aminocyclitol component and a mode of antibacterial action that was also shown to differ somewhat from the mode of action of gentamicin-type antibiotics. When the resistance genes sgm and grm were cloned in Streptomyces lividans and E. coli, they conferred resistance to the expected aminoglycoside compounds but not to hygromycin B. In contrast, introduction of the same resistance genes to M. melanosporea produced resistance to hygromycin B as well. Such an apparent strain dependence in the expression of hygromycin B resistance was also observed with other genes from related genera that are also responsible for aminoglycoside resistance due to methylation of 16S rRNA: of these genes, only kgm assisted expression of hygromycin B resistance and only in the background of M. melanosporea. A possible mechanism for the background dependent of hygromycin B resistance is discussed.

Cloning and characterisation of the rpoS gene from plant growth-promoting Pseudomonas putida WCS358: RpoS is not involved in siderophore and homoserine lactone production

The rpoS gene which encodes a stationary phase sigma factor has been identified and characterised from the rhizosphere-colonising plant growth-promoting Pseudomonas putida strain WCS358. The predicted protein sequence has extensive homologies with the RpoS proteins form other bacteria, in particular with the RpoS sigma factors of the fluorescent pseudomonads. A genomic transposon insertion in the rpoS gene was constructed, these mutants were analysed for their ability to produce siderophore (iron-transport agent) and the autoinducer quorum-sensing molecules called homoserine lactones (AHL). It was determined that RpoS was not involved in the regulation of siderophore and AHL production, synthesis of these molecules is important for gene expression at stationary phase. P. putida WCS358 produces at least three different AHL molecules.

Characterization of natural isolate Lactobacillus acidophilus BGRA43 useful for acidophilus milk production

Lactobacillus acidophilus BGRA43 was selected from a set of human origin isolates of Lact. acidophilus strains for the highest growth rates and antagonistic effect against both Gram-positive and Gram-negative bacteria. The strain BGRA43 also exhibited an inhibitory effect on the growth of Clostridium sporogenes. Inhibition of this strain seems to be due to lactic acid production rather than hydrogen peroxide or bacteriocin. Growth of Lact. acidophilus BGRA43 in non-fat skim milk for 6 h at 37 degrees C resulted in a lowering of the pH value to 4.53. Besides the fast acidification, this strain generated a high viscosity of skim milk. These characteristics make the strain BGRA43 attractive for acidophilus milk production. Lactobacillus acidophilus BGRA43 produces an extracellular proteinase. Whole cells efficiently degraded casein for 3 h at 37 degrees C especially alpha- and beta-casein fractions. Total DNA isolated from the strain BGRA43 did not show any hybridization with lactococcal proteinase probes indicating that this strain produces a distinctive proteinase.

Translational autoregulation of the sgm gene from Micromonospora zionensis

The sisomicin-gentamicin resistance methylase gene (sgm) from Micromonospora zionensis (the producer of antibiotic G-52 [6-N-methyl-sisomicin]) encodes an enzyme that modifies 16S rRNA and thereby confers resistance to 4,6-disubstituted deoxystreptamine aminoglycosides. Here, we report that this gene is regulated on the translational level. The Escherichia coli lacZ gene and operon fusion system was used, and it was shown that an extra copy of the sgm gene decreases the activity of the fusion protein. These results suggested that expression of the sgm gene is regulated by the translational autorepression because of binding of the methylase to its own mRNA. It was shown by computer analysis that the same hexanucleotide (CCGCCC) is present 14 bp before the ribosome-binding site and in the C-1400 region of 16S rRNA, i.e., the region in which most of the aminoglycosides act. A deletion that removes the hexanucleotide before the gene fusion is not prone to negative autoregulation. This mode of regulation of the sgm gene ensures that enough methylase molecules protect the cell from the action of its own antibiotic. On the other hand, if all of the ribosomes are modified, Sgm methylase binds to its own mRNA in an autorepressive manner.

Cloning and characterization of an aminoglycoside resistance determinant from Micromonospora zionensis

The sisomicin-gentamicin resistance methylase (sgm) gene was isolated from Micromonospora zionensis and cloned in Streptomyces lividans. The sgm gene was expressed in Micromonospora melanosporea, where its own promoter was active, and also in Escherichia coli under the control of the lacZ promoter. The complete nucleotide sequence of 1,122 bp and a transcription start point were determined. The sequence contains an open reading frame that encodes a polypeptide of 274 amino acids. The methylation of 30S ribosomal subunits by Sgm methylase accounts adequately for all known resistance characteristics of M. zionensis, but expression of high-level resistance to hygromycin B is background dependent. A comparison of the amino acid sequence of the predicted Sgm protein with the deduced amino acid sequences for the 16S rRNA methylases showed extensive similarity of Grm and significant similarity to KgmB but not to KamB methylase.

Analysis of exopolysaccharide production by Lactobacillus casei CG11, isolated from cheese

Exopolysaccharide-producing Lactobacillus casei CG11 was isolated from soft, white, homemade cheese. In basal minimal medium, it produces a neutral heteropolysaccharide consisting predominantly of glucose (about 75%) and rhamnose (about 15%). Plasmid curing experiments revealed that exopolysaccharide production by strain CG11 is linked to a plasmid approximately 30 kb in size.

Characterization of the Cell Wall-Bound Proteinase of Lactobacillus casei HN14

Lactobacillus casei HN14, which was isolated from homemade cheese, produces an extracellular, cell wall-bound proteinase. The HN14 proteinase can be removed from the cell envelope by washing the cells in a Ca 2+ -free buffer. The activity of the crude proteinase extract is inhibited by phenylmethylsulfonyl fluoride, showing that the enzyme is a serine-type proteinase. Considering the substrate specificity, the HN14 proteinase is similar to the lactococcal PI-type enzyme, since it hydrolyzes β-casein only. Lactobacillus casei HN14 appeared to be plasmid free, which suggests that the proteinase gene is chromosomally located. Chromosomal DNA of this strain hybridizes with DNA probes Q1 (which contains a fragment of the prtM gene) and Q6 and Q92 (which contain fragments of the prtP gene); all three probes originated from the proteinase gene region of Lactococcus lactis subsp. cremoris Wg2. A restriction enzyme map of the proteinase region of Lactobacillus casei HN14 was constructed on the basis of hybridization experiments. Comparison of the restriction enzyme maps of the Lactobacillus casei HN14 proteinase gene region and those of lactococcal proteinase gene regions studied so far indicates that they are highly similar.

Bacteriocin-Producing Strain of Lactococcus lactis subsp. diacitilactis S50

Lactococcus lactis subsp. diacitilactis S50 produces a bacteriocin, designated bacteriocin S50, which has a narrow antibacterial spectrum. It was active only against Lactococcus species, including a nisin producer exhibiting a bactericidal effect. The activity of bacteriocin S50 was sensitive to proteases. It retained antimicrobial activity after being heated to 100°C for up to 60 min and in the pH range 2 to 11.