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  • 1
    Electronic Resource
    Electronic Resource
    Structuring and automating hardware proofs in a higher-order theorem-proving environment (1993)
    Springer
    Formal methods in system design 2 (1993), S. 165-223 
    Details
    ISSN: 1572-8102
    Keywords: hardware verification ; higher-order logic
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science
    Notes: Abstract In this article we present a structured approach to formal hardware verification by modeling circuits at the register-transfer level using a restricted form of higher-order logic. This restricted form of higher-order logic is sufficient for obtaining succinct descriptions of hierarchically designed register-transfer circuits. By exploiting the structure of the underlying hardware proofs and limiting the form of descriptions used, we have attained nearly complete automation in proving the equivalences of the specifications and implementations. A hardware-specific tool called MEPHISTO converts the original goal into a set of simpler subgoals, which are then automatically solved by a general-purpose, first-order prover called FAUST. Furthermore, the complete verification framework is being integrated within a commercial VLSI CAD framework.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01383880
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  • 2
    Electronic Resource
    Electronic Resource
    Accelerating tableaux proofs using compact representations (1994)
    Springer
    Formal methods in system design 5 (1994), S. 145-176 
    Details
    ISSN: 1572-8102
    Keywords: Automated theorem proving ; mathematical logic
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science
    Notes: Abstract In this article a modified form of tableau calculus, calledTableau Graph Calculus, is presented for overcoming the well-known inefficiencies of the traditional tableau calculus to a large extent. This calculus is based on a compact representation of analytic tableaux by using graph structures calledtableau graphs. These graphs are obtained from the input formula in linear time and incorporate most of the rule applications of normal tableau calculus during the conversion process. The size of this representation is linear with respect to the length of the input formula and the graph closely resembles the proof tree of tableau calculi thus retaining the naturalness of the proof procedure. As a result of this preprocessing step, tableau graph calculus has only a single rule which is repeatedly applied to obtain a proof. Many optimizations for the applications of this rule, to effectively prune the search space, are presented as well. Brief details of an implemented prover called FAUST, embedded within the higher-order theorem prover called HOL, are also given. Applications of FAUST within a hardware verification context are also sketched.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01384237
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  • 3
    Electronic Resource
    Electronic Resource
    EPR and Mössbauer spectroscopic studies on the tetrameric, NAD-linked hydrogenase of Nocardia opaca 1b and its two dimers: 1. The βδ-dimer—a prototype of a simple hydrogenase (1995)
    Springer
    BioMetals 8 (1995), S. 149-162 
    Details
    ISSN: 1572-8773
    Keywords: hydrogenase (or H2:NAD+ oxidoreductase, EC 1.12.1.2) ; Nocardia opaca ; diaphorase-dimer ; hydrogenase-dimer ; EPR and Mössbauer spectroscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract The cytoplasmic, tetrameric NAD-linked hydrogenase from Nocardia opaca 1b can be separated in two dimeric substructures, an αγ-dimer with NADH:electron acceptor oxidoreductase (diaphorase) activity and a βδ-dimer which displays hydrogenase activity with artificial electron carriers. These two dimers were preparatively isolated by a FPLC Mono Q procedure in the absence of nickel and at alkaline pH values. The hydrogenase-active βδ-dimer contained, as analyzed by inductively coupled plasma mass spectrometry (ICP-MS), 3.5–3.9 iron atoms and 1.3–1.7 nickel atoms per dimer molecule. EPR and Mössbauer spectra indicated the presence of a [4Fe-4S] cluster. This center turned out to be extremely labile towards oxidants. Oxidation led to irreversible convertion into a [3Fe-4S] form, thus representing an artifact and not a regulatory state of the cluster. The midpoint redox potential of the [4Fe-4S] cluster was determined to be -385 mV. Very weak EPR Ni signals of the βδ-dimer were detectable in the oxidized as well as in the reduced state. The diaphorase-active αγ-dimer was free of nickel and the iron content corresponded to 11.2–12.8 Fe atoms per dimer molecule. From EPR and Mössbauer measurements it was concluded that this dimer contained two [4Fe-4S] clusters, one [2Fe-2S] and one [3Fe-4S] cluster. In accordance with the results obtained for the dimer proteins, for the whole enzyme an iron content of 15.8–16.2 atoms per enzyme molecule have been determined. EPR spectra and spectrum simulations of the native hydrogenase corroborate the cluster assignments of the two dimers: in total the enzyme contains one [2Fe-2S] cluster, one [3Fe-4S] cluster and three [4Fe-4S] clusters.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00142015
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  • 4
    Electronic Resource
    Electronic Resource
    Hydrogen production using chloroplast membranes without oxygen scavengers: An assay with hydrogenases from aerobic hydrogen-oxidizing bacteria and flavodoxins from Desulfovibrio sp. (1983)
    Springer
    Applied microbiology and biotechnology 17 (1983), S. 158-162 
    Details
    ISSN: 1432-0614
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary Electron carrier proteins from Desulfovibrio sp., especially flavodoxins, have been tested as electron mediator between spinach chloroplast membranes and hydrogenase from aerobic hydrogen-oxidizing bacteria. Due to the slow electron transfer between flavodoxin and hydrogenase the rate of hydrogen production is low. However, the classical dramatic decrease of the hydrogen evolution rate in the absence of any oxygen scavengers is not observed when dealing with flavodoxin from Desulfovibrio desulfuricans strain 27774, and the NAD-reducing hydrogenase from Nocardia opaca 1b.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00505881
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  • 5
    Electronic Resource
    Electronic Resource
    Localization and stability of hydrogenases from aerobic hydrogen bacteria (1977)
    Springer
    Archives of microbiology 112 (1977), S. 229-238 
    Details
    ISSN: 1432-072X
    Keywords: Hydrogen bacteria ; Hydrogenase ; Localization ; Membrane bound enzymes ; NAD reduction ; Stability
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Alcaligenes eutrophus strains H 16, B 19, G 27 and N9A contained two different hydrogenases. One enzyme catalyzed the reduction of NAD by hydrogen and was strictly localized in the soluble cell fraction, while the second enzyme was found to be particulate and unable to react with NAD. All other tested strains, Alcaligenes paradoxus SA 29, Pseudomonas facilis, P. palleronii RH 2, Pseudomonas sp. strain GA 3, Paracoccus denitrificans, Aquaspirillum autotrophicum SA 32, and Corynebacterium autotrophicum 14g and 7C contained only a single enzyme exclusively bound to membranes. This was established using fractional centrifugation, indicator enzyme systems, gentle methods of cell disintegration and discontinuous sucrose density gradient centrifugation. In cell-free extracts obtained by rough disruption (sonication) of cells, hydrogenase was associated to particles of different size and sedimentation velocity. A partial solubilization of hydrogenase caused by sonication was observed with P. facilis. Without exception, the particulate hydrogenases were found (1) to be unable to reduce pyridine nucleotides, and (2) to reduce methylene blue at an extremely high activity. The eminent reaction rate of 34 μmoles H2 oxidized per min and mg protein has been determined in particle suspensions of Pseudomonas sp. strain GA 3. All hydrogenases were stable during storage under hydrogen atmosphere, except the soluble enzyme from A. eutrophus H 16 which was shown to be more stable under aerobic conditions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00413086
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  • 6
    Electronic Resource
    Electronic Resource
    The NAD-linked soluble hydrogenase from Alcaligenes eutrophus H16: detection and characterization of EPR signals deriving from nickel and flavin (1996)
    Springer
    JBIC 1 (1996), S. 99-110 
    Details
    ISSN: 1432-1327
    Keywords: Key words Alcaligenes eutrophus ; Hydrogenase ; EPR spectroscopy ; Nickel centre ; Iron-sulfur cluster
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  In this study we confirmed the previous observation that the cytoplasmic NAD-linked hydrogenase of Alcaligenes eutrophus H16 is EPR-silent in the oxidized state. We also demonstrated the presence of significant Ni-EPR signals when the enzyme was either reduced with the natural electron carrier NADH (5–10 mM) or carefully titrated with sodium dithionite to an intermediate, narrow redox potential range (–280 to –350 mV). Reduction with NADH under argon atmosphere led to a complex EPR spectrum at 80 K with g values at 2.28, 2.20, 2.14, 2.10, 2.05, 2.01 and 2.00. This spectrum could be differentiated by special light/dark treatments into three distinct signals: (1) the "classical" Ni-C signal with g values at 2.20, 2.14 and 2.01, observed with many hydrogenases in the reduced, active state; (2) the light-induced signal (Ni-L) with g values at 2.28, 2.10 and 2.05 and (3) a flavin radical (FMN semiquinone) signal at g = 2.00. The assignment of the Ni-EPR signal was clearly confirmed by EPR spectra of hydrogenase labeled with 61Ni (nuclear spin I = 3/2) yielding a broadening of the Ni spectra at all g values and a resolved 61Ni hyperfine splitting into four lines of the low field edge in the case of the light-induced Ni-EPR signal. The redox potentials determined at pH 7.0 for the described redox components were: for FMN –170 mV (midpoint potential, Em, for appearance), –200 mV (EPR signal intensity maximum) and –230 mV (Em for disappearance); for the Ni centre (Ni-C), –290 mV (Em for appearance), –305 mV (signal intensity maximum) and –325 mV (Em for disappearance). Exposure of the NADH-reduced hydrogenase to carbon monoxide led to an apparent Ni-CO species indicated by a novel rhombic EPR signal with g values at 2.35, 2.08 and 2.01.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007750050028
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  • 7
    Electronic Resource
    Electronic Resource
    Model reduction by extended quasi-steady-state approximation (2000)
    Springer
    Journal of mathematical biology 40 (2000), S. 443-450 
    Details
    ISSN: 1432-1416
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract. We extend the quasi-steady-state approximation (QSSA) with respect to the class of differential systems as well as with respect to the order of approximation. We illustrate the first extension by an example which cannot be treated in the frame of the classical approach. As an application of the second extension we prove that the trimolecular autocatalator can be approximated by a fast bimolecular reaction system. Finally we describe a class of singularly perturbed systems for which a higher order QSSA can easily be obtained.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002850000026
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  • 8
    Electronic Resource
    Electronic Resource
    Plasmid pAO1 of Arthrobacter oxidans encodes 6-hydroxy-d-nicotine oxidase: cloning and expression of the gene in Escherichia coli (1986)
    Springer
    Molecular genetics and genomics 202 (1986), S. 96-101 
    Details
    ISSN: 1617-4623
    Keywords: Arthrobacter oxidans ; Catabolic plasmids ; Nicotin degradation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The 160 kb plasmid pAO1 from Arthrobacter oxidans (Brandsch and Decker 1984) was subcloned in Escherichia coli with the aid of the plasmid vectors pUR222 and pBR322. Screening of the recombinant clones for enzyme activity revealed that the flavoenzyme 6-hydroxy-d-nicotine oxidase (6-HDNO), one of the enzymes of the nicotine-degradative pathway in A. oxidans, is encoded on pAO1. Immunoprecipitation of 35S-methionine-labelled E. coli cells with 6-HDNO-specific antiserum and expression of recombinant plasmid DNA in E. coli “maxicells” revealed that 6-HDNO is made as a 52,000 dalton protein, approximately 4,500 daltons larger than 6-HDNO from A. oxidans. The 6-HDNO activity was constitutively expressed in E. coli cells, possibly from an A. oxidans promoter, as shown by subcloning of the 6-HDNO gene in pBR322, using the expression vector pKK223-3 and the promoter probe vector pCB192.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00330523
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  • 9
    Electronic Resource
    Electronic Resource
    Autotrophic growth of strains ofRhizobium and properties of isolated hydrogenase (1984)
    Springer
    Current microbiology 10 (1984), S. 49-52 
    Details
    ISSN: 1432-0991
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Four strains ofRhizobium (R. trifolii RCL10,R. japonicum S19 and SB16, andRhizobium sp. NEA4) were demonstrated to grow lithoautotrophically with molecular hydrogen as sole electron donor and with ammonium or with N2 as N source. All of them showed ribulose-1,5-bisphosphate carboxylase activity and hydrogenase (H2-uptake) activity with methylene blue and oxygen as electron acceptors. ForR. japonicum SB 16, a doubling time under autotrophic conditions of 30 h and a specific hydrogenase activity (methylene blue reduction) in crude extracts of 1.4 U/mg protein were calculated.Rhizobium hydrogenase is a membrane-bound enzyme. It is mainly detectable in particulate cell fractions, it cross-reacts with the antibodies of the membrane-bound hydrogenase ofAlcaligenes eutrophus, and is unable to reduce NAD. The isolated hydrogenase is a relatively oxygen-sensitive enzyme with a half-life of three days when stored at 4°C under air.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01576047
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  • 10
    Electronic Resource
    Electronic Resource
    Autotrophic growth of nitrogen-fixingAzospirillum species and partial characterization of hydrogenase from strain CC (1986)
    Springer
    Current microbiology 13 (1986), S. 291-297 
    Details
    ISSN: 1432-0991
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Out of 15 strains ofAzospirillum spp. isolated from the roots of different plants, only 4 (CY, M, CC, and AM) were able to grow autotrophically with H2 and CO2. All of them showed H2 uptake in the presence of oxygen or methylene blue and ribulose-1,5-bisphosphate carboxylase activity. Among the four strains, strain CC isolated from the roots ofCenchrus cilliaris showed maximum H2+O2 uptake (32.5 μl/min. mg protein) as well as H2 uptake in the presence of methylene blue (41.4 μl/min·mg protein) and also the maximum activity of ribulose-1,5-bisphosphate carboxylase (17 units [U]/g protein). The doubling time of this strain under autotrophic growth conditions and at low oxygen concentration (2.5%, vol/vol) was 10 h. At the same O2 concentration the maximal rates of H2+O2 uptake were reached. The distribution of hydrogenase activity among soluble and particulate protein fractions revealed that the hydrogenase ofAzospirillum strain CC is a membrane-bound enzyme. It showed cross-reaction with antibodies raised against the membrane-bound hydrogenase ofAlcaligenes eutrophus. The hydrogenase in intact cells and crude extracts reacted with methylene blue, phenazine methosulfate, and ferricyanide, but not with NAD or FMN. The specific hydrogenase activity, with methylene blue as an acceptor, was 5.71 U/mg protein in crude extract at 9.38 U/mg protein in the membrane suspension. Hydrogen evolution from reduced viologen dyes could not be demonstrated. The hydrogenase is oxygen sensitive and can be optimally stabilized by addition of dithionite to H2-gased samples.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01577194
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