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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
    Adhesion-contractile balance in myocyte differentiation
    (2004-11-02) Griffin, Maureen A.; Sen, Shamik; Sweeney, H. Lee; Discher, Dennis E
    Tissue cells generally pull on their matrix attachments and balance a quasi-static contractility against adequate adhesion, but any correlation with and/or influence on phenotype are not yet understood. Here, we begin to demonstrate how differentiation state couples to actomyosin-based contractility through adhesion and substrate compliance. Myotubes are differentiated from myoblasts on collagen-patterned coverslips that allow linear fusion but prevent classic myotube branching. Postfusion, myotubes adhere to the micro-strips but lock into a stress fiber-rich state and do not differentiate significantly further. In contrast, myotubes grown on top of such cells do progress through differentiation, exhibiting actomyosin striations within one week. A compliant adhesion to these lower cells is suggested to couple to contractility and accommodate the reorganization needed for upper cell striation. Contractility is assessed in these adherent cells by mechanically detaching one end of the myotubes. All myotubes, whether striated or not, shorten with an exponential decay. The cell-on-cell myotubes relax more, which implies a greater contractile stress. The non-muscle myosin II inhibitor blebbistatin inhibits relaxation for either case. Myotubes in culture are thus clearly prestressed by myosin II, and this contractility couples to substrate compliance and ultimately influences actomyosin striation.
  • Publication
    Subharmonic Behavior of Phospholipid-coated Ultrasound Contrast Agent Microbubbles
    (2010-11-01) Sijl, Jeroen; Dollet, Benjamin; Overvelde, Marlies; Garbin, Valeria; Rozendal, Timo; deJong, Nico; Lohse, Detlef; Versluis, Michel
    Coated microbubbles, unlike tissue are able to scatter sound subharmonically. Therefore, the subharmonic behavior of coated microbubbles can be used to enhance the contrast in ultrasound contrast imaging. Theoretically, a threshold amplitude of the driving pressure can be calculated above which subharmonic oscillations of microbubbles are initiated. Interestingly, earlier experimental studies on coated microbubbles demonstrated that the threshold for these bubbles is much lower than predicted by the traditional linear viscoelastic shell models. This paper presents an experimental study on the subharmonic behavior of differently sized individual phospholipid coated microbubbles. The radial subharmonic response of the microbubbles was recorded with the Brandaris ultra high-speed camera as a function of both the amplitude and the frequency of the driving pulse. Threshold pressures for subharmonic generation as low as 5 kPa were found near a driving frequency equal to twice the resonance frequency of the bubble. An explanation for this low threshold pressure is provided by the shell buckling model proposed by Marmottant et al. [J. Acoust. Soc. Am. 118, 3499–3505 (2005)]. It is shown that the change in the elasticity of the bubble shell as a function of bubble radius as proposed in this model, enhances the subharmonic behavior of the microbubbles.
  • Publication
    A Study of Carbon Formation and Prevention in Hydrocarbon-Fueled SOFC
    (2006-04-21) Kim, Taeyoon; Liu, G.; Boaro, Marta; Vohs, John M; Lee, S.-I.; Gorte, Raymond J; Al-Madhi, O. H; Dabbousi, B. O.
    The formation and removal of the carbonaceous deposits formed by n-butane and liquid hydrocarbons, such as n-decane and proprietary light and heavy naphthas, between 973 and 1073 K on YSZ and ceria-YSZ, has been studied to determine conditions for stable operation of direct-utilization SOFC. First, it is shown that deactivation of SOFC with Cu-ceria-YSZ anodes operating on undiluted n-decane, a mixture of 80% n-decane and 20% toluene, or light naphtha at temperatures above 973 K is due to filling of the pores with polyaromatic compounds formed by gas-phase, free-radical reactions. Formation of these compounds occurs at a negligible rate below 973 K but increases rapidly above this temperature. The rate of formation also depends on the residence time of the fuel in the anode compartment. Because steam does not participate in the gas-phase reactions, carbonaceous deposits could form even at a H2O:C ratio of 1.5, a value greater than the stability threshold predicted by thermodynamic calculations. Temperature-programmed-oxidation (TPO) measurements with 20% H2O in He demonstrated that carbon deposits formed in pure YSZ were unreactive below 1073 K, while deposits formed on ceria-YSZ could be removed at temperatures as low as 923 K. Based on these results, we discuss strategies for avoiding carbon formation during the operation of direct-utilization anodes on oil-based liquid fuels.
  • Publication
    A Comparison of Molten Sn and Bi for Solid Oxide Fuel Cell Anodes
    (2010-01-19) Jayakumar, Abhimanyu; Vohs, John M; Lee,; Gorte, Raymond J; Hornés,
    Molten Sn and Bi were examined at 973 and 1073 K for use as anodes in solid oxide fuel cells with yttria-stabilized zirconia (YSZ) electrolytes. Cells were operated under "battery" conditions, with dry He flow in the anode compartment, to characterize the electrochemical oxidation of the metals at the YSZ interface. For both metals, the open-circuit voltages (OCVs) were close to that expected based on their oxidation thermodynamics, ~0.93 V for Sn and ~0.48 V for Bi. With Sn, the cell performance degraded rapidly after the transfer of approximately 0.5-1.5 C/cm2 of charge due to the formation of a SnO2 layer at the YSZ interface. At 973 K, the anode impedance at OCV for freshly reduced Sn was approximately 3 Ω cm2 but this increased to well over 250 Ω cm2 after the transfer of 1.6 C/cm2 of charge. Following the transfer of 8.2 C/cm2 at 1073 K, the formation of a 10 µm thick SnO2 layer was confirmed by scanning electron microscopy. With Bi, the OCV anode impedance at 973 K was less than 0.25 Ω cm2 and remained constant until essentially all of the Bi had been oxidized to Bi2O3. Some implications of these results for direct carbon fuel cells are discussed.
  • Publication
    Influence of Composition and Cu Impregnation Method on the Performance of Cu/CeO2/YSZ SOFC Anodes
    (2006-03-09) Jung, Sukwon; Lu, Chun; He, Hongpeng; Gorte, Raymond J; Ahn, Kipyung; Vohs, John M
    In this study, we report on how different impregnation procedures affect the distribution and morphology of the Cu component in Cu/CeO2/YSZ composite anodes and how this affects anode performance. Two different methods for Cu addition to the porous YSZ anode were investigated: impregnation using aqueous solutions of Cu(NO3)2 and impregnation using aqueous solutions of Cu(NO3)2 plus urea. The latter method produced a homogeneous distribution of Cu throughout the anode while the former resulted in a higher concentration of Cu near the exposed surface relative to that in the bulk. Studies of the thermal stability of the deposited copper layers, and the influence of the Cu distribution on cell performance when operating with humidified H2 as the fuel are also presented.