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Now showing 1 - 10 of 172
  • Publication
    Candida Albicans Stimulates Streptococcus Mutans Microcolony Development via Cross-Kingdom Biofilm-Derived Metabolites
    (2017-01-30) Kim, Dongyeop; Sengupta, Arjun; Niepa, Tagbo H. R; Lee, Byung-Hoo; Weljie, Aalim; Freitas-Blanco, Veronica S; Murata, Ramiro M; Stebe, Kathleen J; Lee, Daeyeon; Koo, Hyun
    Candida albicans is frequently detected with heavy infection of Streptococcus mutans in plaque-biofilms from children affected with early-childhood caries, a prevalent and costly oral disease. The presence of C. albicans enhances S. mutans growth within biofilms, yet the chemical interactions associated with bacterial accumulation remain unclear. Thus, this study was conducted to investigate how microbial products from this cross-kingdom association modulate S. mutans build-up in biofilms. Our data revealed that bacterial-fungal derived conditioned medium (BF-CM) significantly increased the growth of S. mutans and altered biofilm 3D-architecture in a dose-dependent manner, resulting in enlarged and densely packed bacterial cell-clusters (microcolonies). Intriguingly, BF-CM induced S. mutans gtfBC expression (responsible for Gtf exoenzymes production), enhancing Gtf activity essential for microcolony development. Using a recently developed nanoculture system, the data demonstrated simultaneous microcolony growth and gtfB activation in situ by BF-CM. Further metabolites/chromatographic analyses of BF-CM revealed elevated amounts of formate and the presence of Candida-derived farnesol, which is commonly known to exhibit antibacterial activity. Unexpectedly, at the levels detected (25–50 μM), farnesol enhanced S. mutans-biofilm cell growth, microcolony development, and Gtf activity akin to BF-CM bioactivity. Altogether, the data provide new insights on how extracellular microbial products from cross-kingdom interactions stimulate the accumulation of a bacterial pathogen within biofilms.
  • Publication
    Interaction of Platinum Films with the (0001#) and (0001) Surfaces of ZnO
    (1994) Petrie, W. T; Vohs, John M
    In this investigation, the growth, structure, and electronic properties of Pt films on the polar surfaces of ZnO were examined using high-resolution electron energy-loss spectroscopy (HREELS) and low-energhy, electron diffraction (LEED). The growth mode of vapor-deposited Pt films on ZnO(0001#) and ZnO(0001) at 300 K was found to be nearly layer-by-layer. The surfaces of Pt films produced in this manner exhibited hexagonal symmetry and were stable up to 600 K. At higher temperatures, the Pt agglomerated into particles which remained oriented with respect to the ZnO substrate. HREELS results indicate that there are only weak interactions at the Pt/ZnO(0001#) interface, while charge transfer and Schottky barrier formation occures at the Pt/ZnO(0001) interface.
  • Publication
    Microbial Nanoculture as an Artificial Microniche
    (2016-08-01) Niepa, Tagbo H. R; Hou, Likai; Goulian, Mark; Jiang, Hongyuan; Koo, Hyun; Lee, Daeyeon; Stebe, Kathleen J
    Microbes self-organize in microcolonies while transitioning to a sessile form within a protective biofilm matrix. To enable the detailed study of microbial dynamics within these microcolonies, new sessile culture systems are needed that sequester cells and mimic their complex growth conditions and interactions. We present a new nanoliter-scale sessile culture system that is easily implemented via microfluidics-enabled fabrication. Hundreds of thousands of these nanocultures can be easily generated and imaged using conventional or confocal microscopy. Each nanoculture begins as a several nanoliter droplet of suspended cells, encapsulated by a polydimethylsiloxane (PDMS) membrane. The PDMS shell provides long-lasting mechanical support, enabling long term study, and is selectively permeable to small molecules including antibiotics, signaling molecules and functional fluorescent probes. Thus, as microcolonies mature within the nanocultures, they can be stressed or interrogated using selected probes to characterize cell physiological properties, antibiotic susceptibilities, and antagonistic interactions. We demonstrate this platform by investigating broad ranges of microcolony dynamics, including direct and indirect bacterial-fungal interactions. This versatile new tool has broad potential for addressing biological questions associated with drug resistance, chronic infections, microbiome dynamics, and antibiotic discovery.
  • Publication
    Inexpensive Ultrahigh Vacuum Heatable/Coolable xyz-Rotary Motion Sample Manipulator
    (1995) Peterson, Susan L; Schulz, Kirk H; Schulz, Carl A; Vohs, John M
    A simple design for a heatable, coolable, rotable sample manipulator, suitable for ultrahigh vacuum (UHV) applications, is described. Highlights of the design include using a combination power/thermocouple feedthrough for heating, cooling, and temperature measurement; and the use of primarily "off-the-shelf" components available from most UHV components vendors. The described manipulator is capable of sample cooling to ~100 K, sample heating to above 900 K, while maintaining 360o of rotary motion, ~1 in. of x and y motion, and 2 in. of z motion. The apparatus can be assembled for approximately $5500 (all new parts) and uses about 3 l of liquid N2 per day. © 1995 American Institute of Physics.
  • Publication
    Progress in the development and application of computational methods for probabilistic protein design
    (2004-07-06) Park, Sheldon; Wang, Wei; Boder, Eric T.; Saven, Jeffery G.; Kono, Hidetoshi
    Proteins exhibit a wide range of physical and chemical properties, including highly selective molecular recognition and catalysis, and are also key components in biological metabolic, catabolic, and signaling pathways. Given that proteins are well-structured and can now be rapidly synthesized, they are excellent targets for engineering of both molecular structure and biological function. Computational analysis of the protein design problem allows scientists to explore sequence space and systematically discover novel protein molecules. Nonetheless, the complexity of proteins, the subtlety of the determinants of folding, and the exponentially large number of possible sequences impede the search for peptide sequences compatible with a desired structure and function. Directed search algorithms, which identify directly a small number of sequences, have achieved some success in identifying sequences with desired structures and functions. Alternatively, one can adopt a probabilistic approach. Instead of a finite number of sequences, such calculations result in a probabilistic description of the sequence ensemble. In particular, by casting the formalism in the language of statistical mechanics, the site-specific amino acid probabilities of sequences compatible with a target structure may be readily identified. The computational probabilities are well suited for both de novo protein design of particular sequences as well as combinatorial, library-based protein engineering. The computed site-specific amino acid profile may be converted to a nucleotide base distribution to allow assembly of a partially randomized gene library. The ability to synthesize readily such degenerate oligonucleotide sequences according to the prescribed distribution is key to constructing a biased peptide library genuinely reflective of the computational design. Herein we illustrate how a standard DNA synthesizer can be used with only a slight modification to the synthesis protocol to generate a pool of degenerate DNA sequences, which encodes a predetermined amino acid distribution with high fidelity.
  • Publication
    Elastic instability of polymer-shelled bubbles formed from air-in-oil-in-water compound bubbles
    (2010-07-09) Lee, Myung Han; Lee, Daeyeon
    We study the stability of polymer-shelled bubbles with controlled dimensions generated from air-in-oil-in-water (A/O/W) compound bubbles. We show that the ratio of the shell thickness to bubble radius is critical in generating un-deformed polymer-shelled bubbles from A/O/W compound bubbles. In addition, the effects of shell stiffness and encapsulated gas on bubble stability are also investigated.
  • Publication
    Role of configurational entropy in the thermodynamics of clusters of point defects in crystalline solids
    (2005-07-20) Kapur, Sumeet S; Crocker, John C; Prasad, Manish; Sinno, Talid
    The internal configurational entropy of point defect clusters in crystalline silicon is studied in detail by analyzing their potential energy landscapes. Both on-lattice and off-lattice calculation approaches are employed to demonstrate the importance of off-lattice configurational states that arise due to a large number of inherent structures (local minima) in the energy landscape generated by the interatomic potential function. The resulting cluster configurational entropy of formation is shown to exhibit behavior that is qualitatively similar to that observed in supercooled liquids and amorphous solids and substantially alters the thermodynamic properties of point defect clusters in crystals at high temperature. This behavior is shown to be independent of interatomic potential and cluster type, and suggests that defects in crystals at high temperature should be generally described by a quasicontinuous collection of nondegenerate states rather than as a single ground state structure. The modified thermodynamic properties of vacancy clusters at high temperature are found to explain a longstanding discrepancy between simulation predictions and experimental measurements of vacancy aggregation dynamics in silicon.
  • Publication
    Analysis of the Performance of the Electrodes in a Natural Gas Assisted Steam Electrolysis Cell
    (2008-02-01) Gorte, Raymond J; Wang, Wensheng; Vohs, John M
    The performance of solid oxide electrolysis (SOE) cells while operating in the natural gas assisted steam electrolysis (NGASE) mode was evaluated. The SOE cells used yttria-stabilized-zirconia (YSZ) as the oxygen ion conducting electrolyte, Co–CeO2–YSZ as the H2–H2O electrode, and Pd-doped CeO2 YSZ source as the CH4-oxidation electrode. The cell electrochemical performance was evaluated as a function of the H2O/H2 ratio and the extent of conversion of CH4. The results of this study provide insight into the factors that control electrode performance and further demonstrate the viability of an NGASE cell for the production of H2.
  • Publication
    Surface probe measurements of the elasticity of sectioned tissue, thin gels and polyelectrolyte multilayer films : correlations between substrate stiffness and cell adhesion
    (2004-10-10) Engler, Adam J; Richert, Ludovic; Wong, Joyce; Discher, Dennis E; Picart, Catherine
    Surface probe measurements of the elasticity of thin-film matrices as well as biological samples prove generally important to understanding cell attachment across such systems. To illustrate this, sectioned arteries were probed by Atomic Force Microscopy (AFM) within the smooth muscle cell (SMC)-rich medial layer, yielding an apparent Young’s modulus Emedia ~ 5-8 kPa. Polyacrylamide gels with Egel spanning several-fold above and below this range were then cast 5-70 μm thick and coated with collagen: SMC spreading shows a hyperbolic dependence in projected cell area versus Egel. The modulus that gives half-max spreading is E1/2-spread ~ 8-10 kPa, proving remarkably close to Emedia. More complex, layer-by-layer micro-films of poly(L-lysine)/hyaluronic acid were also tested and show equivalent trends of increased SMC spreading with increased stiffness. Adhesive spreading of cells thus seems to correlate broadly with the effective stiffness of synthetic materials and tissues.
  • Publication
    An Internally Consistent Approach for Modeling Solid-State Aggregation: II. Mean-Field Representation of Atomistic Processes
    (2003-07-15) Prasad, Manish; Sinno, Talid R
    A detailed continuum (mean-field) model is presented that captures quantitatively the evolution of a vacancy cluster size distribution in crystalline silicon simulated directly by large-scale parallel molecular dynamics. The continuum model is parameterized entirely using the results of atomistic simulations based on the same empirical potential used to perform the atomistic aggregation simulation, leading to an internally consistent comparison across the two scales. It is found that an excellent representation of all measured components of the cluster size distribution can be obtained with consistent parameters only if the assumed physical mechanisms are captured correctly. In particular, the inclusion of vacancy cluster diffusion and a model to capture the dynamic nature of cluster morphology at high temperature are necessary to reproduce the results of the large-scale atomistic simulation. Dynamic clusters with large capture volumes at high temperature, which are the result of rapid cluster shape fluctuations, are shown to be larger than would be expected from static analyses, leading to substantial enhancement of the nucleation rate. Based on these results, it is shown that a parametrically consistent atomistic-continuum comparison can be used as a sensitive framework for formulating accurate continuum models of complex phenomena such as defect aggregation in solids.