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  • 1
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    Phylogenetic Analysis and Classification of the Fungal bHLH Domain (2012)
    Oxford University Press
    Details
    Publication Date: 2012-05-01
    Description: The basic Helix-Loop-Helix (bHLH) domain is an essential highly conserved DNA-binding domain found in many transcription factors in all eukaryotic organisms. The bHLH domain has been well studied in the Animal and Plant Kingdoms but has yet to be characterized within Fungi. Herein, we obtained and evaluated the phylogenetic relationship of 490 fungal-specific bHLH containing proteins from 55 whole genome projects composed of 49 Ascomycota and 6 Basidiomycota organisms. We identified 12 major groupings within Fungi (F1–F12); identifying conserved motifs and functions specific to each group. Several classification models were built to distinguish the 12 groups and elucidate the most discerning sites in the domain. Performance testing on these models, for correct group classification, resulted in a maximum sensitivity and specificity of 98.5% and 99.8%, respectively. We identified 12 highly discerning sites and incorporated those into a set of rules (simplified model) to classify sequences into the correct group. Conservation of amino acid sites and phylogenetic analyses established that like plant bHLH proteins, fungal bHLH–containing proteins are most closely related to animal Group B. The models used in these analyses were incorporated into a software package, the source code for which is available at www.fungalgenomics.ncsu.edu .
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 2
    Electronic Resource
    Electronic Resource
    The Photolysis of Cadmium Dimethyl (1952)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 56 (1952), S. 498-502 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j150496a022
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  • 3
    Electronic Resource
    Electronic Resource
    The Preparation and Some Physical Constants of Cadmium Dimethyl. (1952)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 56 (1952), S. 161-163 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j150494a001
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  • 4
    Electronic Resource
    Electronic Resource
    Quadratic response of a chemical reaction to external oscillations (1992)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 96 (1992), S. 6536-6542 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We develop a second-order response theory to investigate the effects of external periodic perturbations on a chemical reaction at a stable steady state in an open reactor. We apply the theory to the quadratic Schlögl model, a single-variable nonlinear reaction. In the presence of oscillating reactant or product concentrations or oscillating rate coefficients, the average intermediate concentration, the fluxes, and the dissipation are each a Lorentzian function of frequency with midpoint at the inverse relaxation time of the system. Thus even very short relaxation times can be determined by measuring average rates as a function of frequency of the perturbation. The amplitude of the Lorentzian depends on the chemical mechanism of the reaction and is proportional to the square of the amplitude of the applied perturbation. We also show that energy from the perturbation can be used to drive the reaction in a direction opposite of that predicted by the Gibb's free energy difference of reactants and products, even under circumstances where the overall affinity is independent of the perturbation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.462592
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  • 5
    Electronic Resource
    Electronic Resource
    Frequency dependence of catalyzed reactions in a weak oscillating field (1991)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 94 (1991), S. 7414-7419 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The frequency dependence of the average rates of reactions catalyzed by one or more catalysts in a weak oscillating field is derived. The average rates are sums of Lorentzian curves whose characteristic frequencies are the inverse relaxation times of the normal modes of the kinetic system and whose amplitudes are quadratic in the field. The signs of the Lorentz amplitudes can be either positive or negative, so the rates versus frequency can have a variety of shapes, including frequency windows. One can get relaxation times and amplitudes by measuring steady-state rates as a function of the frequency of the field. The theory is applied to determine the Lorentz amplitudes and characteristic frequencies of ion transport rates catalyzed by Na+–K+–ATPase in erythrocytes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.460173
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  • 6
    Electronic Resource
    Electronic Resource
    Nonlinear effect of an oscillating electric field on membrane proteins (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4891-4901 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The nonlinear response of a two-state chemical transition to an oscillating electric field is examined. A reaction for which this analysis is particularly relevant is a conformational transition of a membrane protein exposed to an ac electric field. Even a modest externally applied field leads to a very large local field within the membrane. This gives rise to nonlinear behavior. The applied ac field causes harmonics in the polarization and can cause a dc shift in the state occupancy, both of which can be observed and used to determine kinetic parameters. Fourier coefficients are calculated for the enzyme state probability in the ac field, exactly for infinite frequency, and in powers of the field for finite frequency. Kramers–Kronig relations are proved and response functions are given for the leading terms of the harmonics. The results are extended to the spherical symmetry relevant to suspensions of spherical cells, vesicles, or colloidal particles. If the protein catalyzes a reaction, free energy is transduced from the electric field to the output reaction, even if that reaction is electrically silent. Many transport enzymes are ideal examples. The ac field can cause the enzyme to pump ions or molecules through the membrane against an (electro)chemical potential. The efficiency of this energy transduction can be as high as 25%.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.456728
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  • 7
    Electronic Resource
    Electronic Resource
    Energy transduction between a concentration gradient and an alternating electric field (1990)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 93 (1990), S. 5062-5066 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A four-state transport protein that has electric charges that move concomitantly with conformational changes can transduce energy in either direction between an alternating membrane potential and a concentration gradient. An alternating electric potential of very large amplitude is considered, and the rapid-equilibrium approximation is used for the conformational changes. This permits deriving simple expressions for the transport flux, the power supplied by the alternating potential, and the power applied to the concentration gradient.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.458644
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  • 8
    Electronic Resource
    Electronic Resource
    Overview: The constructive role of noise in fluctuation driven transport and stochastic resonance (1998)
    Woodbury, NY : American Institute of Physics (AIP)
    Chaos 8 (1998), S. 533-538 
    Details
    ISSN: 1089-7682
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Random noise is typically thought of as the enemy of order rather than as a constructive influence. Recent work has shown however that under certain circumstances, noise and Brownian motion can facilitate transmission of information via a mechanism know as stochastic resonance, and help systems use chemical energy and nonequilibrium fluctuations to drive directed motion via fluctuation driven transport. In this focus issue we have collected several articles that capture the flavor of these developing fields and point the way to new directions for research. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.166334
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  • 9
    Electronic Resource
    Electronic Resource
    The Dissociation Constants of Acids in Salt Solutions. II. Acetic Acid (1953)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 75 (1953), S. 586-587 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja01099a019
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  • 10
    Electronic Resource
    Electronic Resource
    The Dissociation Constants of Acids in Salt Solutions. III. Glycolic Acid (1953)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 75 (1953), S. 587-587 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja01099a020
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