Biofilm Biology and Engineering of Geobacter and Shewanella spp. for Energy Applications

Geobacter and Shewanella spp. were discovered in late 1980s as dissimilatory metal-reducing microorganisms that can transfer electrons from cytoplasmic respiratory oxidation reactions to external metal-containing minerals. In addition to mineral-based electron acceptors, Geobacter and Shewanella spp. also can transfer electrons to electrodes. The microorganisms that have abilities to transfer electrons to electrodes are known as exoelectrogens. Because of their remarkable abilities of electron transfer, Geobacter and Shewanella spp. have been the two most well studied groups of exoelectrogens. They are widely used in bioelectrochemical systems (BESs) for various biotechnological applications, such as bioelectricity generation via microbial fuel cells. These applications mostly associate with Geobacter and Shewanella biofilms grown on the surfaces of electrodes. Geobacter and Shewanella biofilms are electrically conductive, which is conferred by matrix-associated electroactive components such as c-type cytochromes and electrically conductive nanowires. The thickness and electroactivity of Geobacter and Shewanella biofilms have a significant impact on electron transfer efficiency in BESs. In this review, we first briefly discuss the roles of planktonic and biofilm-forming Geobacter and Shewanella cells in BESs, and then review biofilm biology with the focus on biofilm development, biofilm matrix, heterogeneity in biofilm and signaling regulatory systems mediating formation of Geobacter and Shewanella biofilms. Finally, we discuss strategies of Geobacter and Shewanella biofilm engineering for improving electron transfer efficiency to obtain enhanced BES performance.

Effect of Matrix Heterogeneity on Cell Mechanosensing

Cells sense mechanical signals within the extracellular matrix, the most familiar being stiffness, but matrix stiffness cannot be simply described by a single value. Randomness in matrix structure causes stiffness...

Elucidating the Role of Matrix Porosity and Rigidity in Glioblastoma Type IV Progression

The highly infiltrating nature of glioma cells is the major cause for the poor prognosis of brain malignancies. Motility, proliferation, and gene expression of cells in natural and synthetic gels have been analyzed by several authors, yet quantitative studies elucidating the role of matrix porosity and rigidity in the development of whole malignant masses are missing. Here, an experimental-computational framework is introduced to analyze the behavior of U87-MG cells and spheroids in compact hyaluronic acid gels (HA), replicating the brain parenchyma; and fibrous collagen gels (COL), resembling the organized structures of the brain. Experimentally it was observed that individual U87-MG cells in COL assumed an elongated morphology within a few hours post inclusion (p.i.) and travelled longer distances than in HA. As spheroids, U87-MG cells rapidly dispersed into COL resulting in infiltrating regions as large as tumor cores (≈600 μm, at 8 days p.i.). Conversely, cells in HA originated smaller and denser infiltrating regions (≈300 μm, at 8 days p.i.). Notably, COL tumor core size was only 20% larger than in HA, at longer time points. Computationally, by introducing for the first time the effects of matrix heterogeneity in our numerical simulations, the results confirmed that matrix porosity and its spatial organization are key factors in priming the infiltrating potential of these malignant cells. The experimental-numerical synergy can be used to predict the behavior of neoplastic masses under diverse conditions and the efficacy of combination therapies simultaneously aiming at killing cancer cells and modulating the tumor microenvironment.

Mechanobiology of Epithelia From the Perspective of Extracellular Matrix Heterogeneity

Understanding the complexity of the extracellular matrix (ECM) and its variability is a necessary step on the way to engineering functional (bio)materials that serve their respective purposes while relying on cell adhesion. Upon adhesion, cells receive messages which contain both biochemical and mechanical information. The main focus of mechanobiology lies in investigating the role of this mechanical coordination in regulating cellular behavior. In recent years, this focus has been additionally shifted toward cell collectives and the understanding of their behavior as a whole mechanical continuum. Collective cell phenomena very much apply to epithelia which are either simple cell-sheets or more complex three-dimensional structures. Researchers have been mostly using the organization of monolayers to observe their collective behavior in well-defined experimental setups in vitro. Nevertheless, recent studies have also reported the impact of ECM remodeling on epithelial morphogenesis in vivo. These new concepts, combined with the knowledge of ECM biochemical complexity are of key importance for engineering new interactive materials to support both epithelial remodeling and homeostasis. In this review, we summarize the structure and heterogeneity of the ECM before discussing its impact on the epithelial mechanobiology.

Life history and matrix heterogeneity interact to shape metapopulation connectivity in spatially structured environments

Metapopulation models have historically treated a landscape as a collection of habitat patches separated by a matrix of uniformly unsuitable habitat. This perspective is still apparent in many studies of marine metapopulations, in which recruitment variation is generally assumed to be primarily the result of variability in ocean currents and interactions with disperser behavior, with little consideration of spatial structure that can affect disperser viability. We use a simple model of dispersal of marine larvae to demonstrate how heterogeneity in dispersal habitat (i.e., the matrix) can generate substantial spatial variation in recruitment. Furthermore, we show how this heterogeneity can interact with larval life-history variation to create alternative patterns of source-sink dynamics. Finally, we place our results in the context of spatially structured matrix population models, and we propose the damping ratio of the connectivity matrix as a general and novel measure of landscape connectivity that may provide conceptual unification to the fields of metapopulation biology and landscape ecology. © 2010 by the Ecological Society of America.

Life history and matrix heterogeneity interact to shape metapopulation connectivity in spatially structured environments

Metapopulation models have historically treated a landscape as a collection of habitat patches separated by a matrix of uniformly unsuitable habitat. This perspective is still apparent in many studies of marine metapopulations, in which recruitment variation is generally assumed to be primarily the result of variability in ocean currents and interactions with disperser behavior, with little consideration of spatial structure that can affect disperser viability. We use a simple model of dispersal of marine larvae to demonstrate how heterogeneity in dispersal habitat (i.e., the matrix) can generate substantial spatial variation in recruitment. Furthermore, we show how this heterogeneity can interact with larval life-history variation to create alternative patterns of source-sink dynamics. Finally, we place our results in the context of spatially structured matrix population models, and we propose the damping ratio of the connectivity matrix as a general and novel measure of landscape connectivity that may provide conceptual unification to the fields of metapopulation biology and landscape ecology. © 2010 by the Ecological Society of America.

Modeling Sand Occurrence in Petroleum Production

This paper presents an advanced model to predict sand occurrence and accurately estimate volumetric sand produced in petroleum production. The sand factors Ks(t), derived from the linear time combination of likelihood of occurrence λm(t) of KRS and KFS, were used to determine sand occurrence and estimate its volumetric production around well bore systems. Therefore, the measured laboratory and field log core data of elastic properties were simulated for the mechanical and hydrodynamic decementation at unobserved multiple field locations of equiprobable realizations. The critical limits for mechanical rock failure and hydrodynamic sand production were defined at sand factors equal to 1 in absolute terms. The sand model results show two distinct gradient points observed for laboratory plots of sand elastic properties: core displacement length defined as the loading point of mechanical rock failure and the flooding point for hydrodynamic fluidized incipient sand production. However, plots of elastic properties with the core length for field case show significant deviations with multiple loading rock failure and flooding sand production points most likely caused by the complex nature of rock matrix heterogeneity for the fields studied.