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  • Inorganic and Physical Chemistry  (3)
  • Bacillus thuringiensis  (1)
  • Base Sequence  (1)
  • Cytoplasmic inheritance  (1)
  • 1
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    Complete genome sequence of Treponema pallidum, the syphilis spirochete (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-07-17
    Description: The complete genome sequence of Treponema pallidum was determined and shown to be 1,138,006 base pairs containing 1041 predicted coding sequences (open reading frames). Systems for DNA replication, transcription, translation, and repair are intact, but catabolic and biosynthetic activities are minimized. The number of identifiable transporters is small, and no phosphoenolpyruvate:phosphotransferase carbohydrate transporters were found. Potential virulence factors include a family of 12 potential membrane proteins and several putative hemolysins. Comparison of the T. pallidum genome sequence with that of another pathogenic spirochete, Borrelia burgdorferi, the agent of Lyme disease, identified unique and common genes and substantiates the considerable diversity observed among pathogenic spirochetes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fraser, C M -- Norris, S J -- Weinstock, G M -- White, O -- Sutton, G G -- Dodson, R -- Gwinn, M -- Hickey, E K -- Clayton, R -- Ketchum, K A -- Sodergren, E -- Hardham, J M -- McLeod, M P -- Salzberg, S -- Peterson, J -- Khalak, H -- Richardson, D -- Howell, J K -- Chidambaram, M -- Utterback, T -- McDonald, L -- Artiach, P -- Bowman, C -- Cotton, M D -- Fujii, C -- Garland, S -- Hatch, B -- Horst, K -- Roberts, K -- Sandusky, M -- Weidman, J -- Smith, H O -- Venter, J C -- AI31068/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1998 Jul 17;281(5375):375-88.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomic Research, Rockville, MD 20850, USA. tpdb@tigr.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9665876" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/genetics/metabolism ; Base Sequence ; Borrelia burgdorferi Group/genetics ; Carrier Proteins/genetics/metabolism ; DNA Repair/genetics ; DNA Replication/genetics ; DNA Restriction Enzymes/genetics ; Energy Metabolism/genetics ; Genes, Bacterial ; Genes, Regulator ; *Genome, Bacterial ; Heat-Shock Response/genetics ; Lipoproteins/genetics ; Membrane Proteins/genetics ; Molecular Sequence Data ; Movement ; Open Reading Frames ; Oxygen Consumption/genetics ; Protein Biosynthesis ; Recombination, Genetic ; Replication Origin ; *Sequence Analysis, DNA ; Transcription, Genetic ; Treponema pallidum/*genetics/metabolism/pathogenicity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
    Electronic Resource
    Electronic Resource
    Chloroplast DNA variation between species of Triticum and Aegilops. Location of the variation on the chloroplast genome and its relevance to the inheritance and classification of the cytoplasm (1983)
    Springer
    Theoretical and applied genetics 65 (1983), S. 247-262 
    Details
    ISSN: 1432-2242
    Keywords: Triticum ; Aegilops ; Chloroplast DNA ; Cytoplasmic inheritance ; Wheat evolution ; The B genome donor ; Restriction mapping ; Insertions ; Deletions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Restriction endonuclease analysis revealed interspecific and intraspecific variation between the chloroplast DNAs and therefore between the cytoplasms of 14 selected species of Triticum and Aegilops. Eleven distinct chloroplast DNA types were detected, the differences between them residing in the varied combination of a relatively few DNA alterations. The variation was simple enough for chloroplast DNA analysis to be used as a basis for the identification and classification of the Triticum and Aegilops cytoplasms. There was good agreement with the classification based on analysis of the phenotypic effects of the cytoplasm when combined with the T. aestivum nucleus in nuclear-cytoplasmic hybrids (Tsunewaki et al. 1976). There was however no correlation between specific chloroplast DNA alterations and any of the phenotypic effects known to be associated with specific cytoplasms. Although the diploid species examined included all those which have been suggested as possible donors of the cytoplasm and the B genome to T. aestivum, none of the chosen accessions belonged to the same cytoplasmic class as T. aestivum itself, except that of the tetraploid T. dicoccoides. Therefore, none of the diploid accessions analysed was the B genome donor. The analyses did however support several other suggestions which have been made concerning wheat ancestry. Scoring the different chloroplast DNA types according to the rarity of their banding patterns indicated that four of the eleven cytoplasms are of relatively recent origin. The DNA alterations most easily detectable by the limited comparison of the eleven Triticum/Aegilops chloroplast DNA types using only 4 endonucleases were insertions and deletions. These ranged between approximately 50 bp and 1,200 bp in size and most of them were clustered in 2 segments of the large single-copy region of the genome. Only two examples of the loss of restriction endonuclease sites through possible point mutations were observed. No variation was detected in the inverted repeat regions. Several of the deletions and insertions map close to known chloroplast protein genes, and there is also an indication that the more variable regions of the chloroplast genome may contain sequences which have allowed DNA recombination and rearrangement to occur.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00308076
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Biolistic introduction of a synthetic Bt gene into elite maize (1955)
    Springer
    Euphytica 85 (1955), S. 119-123 
    Details
    ISSN: 1573-5060
    Keywords: Bacillus thuringiensis ; maize ; microprojectile bombardment ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary A synthetic Bt gene encoding a truncated version of the CryIA(b) protein derived from Bacillus thuringiensis was successfully introduced into elite maize using microprojectile bombardment of immature embryos. The method used to initiate and identify transformation events is described. We describe the detailed parameters used for the Biolistics device as well as the plasmids used for the transformations. The plasmids contained the synthetic Bt gene driven by either the 35S CaMV promoter or a combination of two tissue-specific promoters, leaf and pollen, derived from maize. Specific conditions for the culture of Type I callus from immature embryos, the phosphinothricin (PPT) selection protocol, and the regeneration of plants are discussed. T0 and T1 plants were initially identified using the pH-dependent chlorophenol red test and/or the histochemical β-glucuronidase (GUS) assay. PCR and Southern data confirm the presence of the 35S CaMV promoter and the synthetic Bt gene.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00023939
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  • 4
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    Evaluation of joint probability density function models for turbulent nonpremixed combustion with complex chemistry (1996)
    In:  CASI
    Details
    Publication Date: 2016-06-07
    Description: Two types of mixing sub-models are evaluated in connection with a joint-scalar probability density function method for turbulent nonpremixed combustion. Model calculations are made and compared to simulation results for homogeneously distributed methane-air reaction zones mixing and reacting in decaying turbulence within a two-dimensional enclosed domain. The comparison is arranged to ensure that both the simulation and model calculations a) make use of exactly the same chemical mechanism, b) do not involve non-unity Lewis number transport of species, and c) are free from radiation loss. The modified Curl mixing sub-model was found to provide superior predictive accuracy over the simple relaxation-to-mean submodel in the case studied. Accuracy to within 10-20% was found for global means of major species and temperature; however, nitric oxide prediction accuracy was lower and highly dependent on the choice of mixing sub-model. Both mixing submodels were found to produce non-physical mixing behavior for mixture fractions removed from the immediate reaction zone. A suggestion for a further modified Curl mixing sub-model is made in connection with earlier work done in the field.
    Keywords: Inorganic and Physical Chemistry
    Type: Studying Turbulence Using Numerical Simulation Databases; Part 6; 167-186; NASA-TM-111953
    Format: application/pdf
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  • 5
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    A new methodology to determine kinetic parameters for one- and two-step chemical models (1996)
    In:  CASI
    Details
    Publication Date: 2016-06-07
    Description: In this paper, a new methodology to determine kinetic parameters for simple chemical models and simple transport properties classically used in DNS of premixed combustion is presented. First, a one-dimensional code is utilized to performed steady unstrained laminar methane-air flame in order to verify intrinsic features of laminar flames such as burning velocity and temperature and concentration profiles. Second, the flame response to steady and unsteady strain in the opposed jet configuration is numerically investigated. It appears that for a well determined set of parameters, one- and two-step mechanisms reproduce the extinction limit of a laminar flame submitted to a steady strain. Computations with the GRI-mech mechanism (177 reactions, 39 species) and multicomponent transport properties are used to validate these simplified models. A sensitivity analysis of the preferential diffusion of heat and reactants when the Lewis number is close to unity indicates that the response of the flame to an oscillating strain is very sensitive to this number. As an application of this methodology, the interaction between a two-dimensional vortex pair and a premixed laminar flame is performed by Direct Numerical Simulation (DNS) using the one- and two-step mechanisms. Comparison with the experimental results of Samaniego et al. (1994) shows a significant improvement in the description of the interaction when the two-step model is used.
    Keywords: Inorganic and Physical Chemistry
    Type: Studying Turbulence Using Numerical Simulation Databases; Part 6; 149-166; NASA-TM-111953
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  • 6
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    Effect of chemistry and turbulence on NO formation in oxygen-natural gas flames (1996)
    In:  CASI
    Details
    Publication Date: 2016-06-07
    Description: The effects of chemistry and turbulence on NO formation in oxygen-natural turbulent diffusion flames gas flames have been investigated. The chemistry of nitric oxides has been studied numerically in the counterflow configuration. Systematic calculations with the GRI 2.11 mechanism for combustion of methane and NO chemistry were conducted to provide a base case. It was shown that the 'simple' Zeldovich mechanism accounts for more than 75% of N2 consumption in the flame in a range of strain-rates varying between 10 and 1000 s-l. The main shortcomings of this mechanism are: 1) overestimation (15%) of the NO production rate at low strain-rates because it does not capture the reburn due to the hydrocarbon chemistry, and 2) underestimation (25%) of the NO production rate at high strainrates because it ignores NO production through the prompt mechanism. Reburn through the Zeldovich mechanism alone proves to be significant at low strain-rates. A one-step model based on the Zeldovich mechanism and including reburn has been developed. It shows good agreement with the GRI mechanism at low strain-rates but underestimates significantly N2 consumption (about 50%) at high strain-rates. The role of turbulence has been assessed by using an existing 3-D DNS data base of a diffusion flame in decaying turbulence. Two PDF closure models used in practical industrial codes for turbulent NO formation have been tested. A simpler version of the global one-step chemical scheme for NO compared to that developed in this study was used to test the closure assumptions of the PDF models, because the data base could not provide all the necessary ingredients. Despite this simplification, it was possible to demonstrate that the current PDF models for NO overestimate significantly the NO production rate due to the fact that they neglect the correlations between the fluctuations in oxygen concentration and temperature. A single scalar PDF model for temperature that accounts for such correlations based on laminar flame considerations has been developed and showed excellent agreement with the values given by the DNS.
    Keywords: Inorganic and Physical Chemistry
    Type: Studying Turbulence Using Numerical Simulation Databases; Part 6; 187-206; NASA-TM-111953
    Format: application/pdf
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