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  • 1
    Electronic Resource
    Electronic Resource
    Electron density and recombination rate measurements in CO-seeded optically pumped plasmas (2001)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 89 (2001), S. 5903-5910 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Electron production rate and electron density in cold optically pumped CO–Ar and CO–N2 plasmas in the presence of small amounts of O2 and NO have been measured using a Thomson discharge probe and microwave attenuation. Nonequilibrium ionization in the plasmas is produced by an associative ionization mechanism in collisions of highly vibrationally excited CO molecules. It is shown that adding small amounts of O2 or NO (50–100 mTorr) to the baseline gas mixtures at P=100 torr results in an increase of the electron density by up to a factor of 20–40 (from ne〈1010 cm−3 to ne=(1.5–3.0)×1011 cm−3). This occurs while the electron production rate either decreases (as in the presence of O2) or remains nearly constant within a factor of 2 (as in the presence of NO). It is also shown that the electron–ion recombination rates inferred from these measurements decrease by two to three orders of magnitude compared to their baseline values (with no additives in the cell), down to β≅1.5×10−8 cm3/s with 50–100 mTorr of oxygen or nitric oxide added to the baseline CO–Ar mixture, and β≅(2 to 3)×10−7 cm3/s with 75–100 mTorr of O2 or NO added to the baseline CO–N2 mixture. The overall electron–ion removal rates in the presence of equal amounts of O2 or NO additives turn out to be very close, which shows that the effect of electron attachment to oxygen at these conditions is negligible. These results suggest a novel method of electron density control in cold laser-sustained steady-state plasmas and open a possibility of sustaining stable high-pressure nonequilibrium plasmas at high electron densities and low plasma power budget. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1359754
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  • 2
    Electronic Resource
    Electronic Resource
    Effect of electron density on shock wave propagation in optically pumped plasmas (2002)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 91 (2002), S. 2604-2610 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: This article discusses experimental studies of spark-generated shock wave propagation in CO-laser sustained optically pumped CO–Ar–O2 plasmas. The rotational-translational temperature of the plasma is measured by Fourier transform infrared emission spectroscopy. The electron density in the plasma is determined by microwave attenuation. The line-of-sight averaged density distribution across the propagating shock is detected by photoacoustic deflection (PAD). The measurements show that adding small amounts of oxygen (up to 0.1%) to the baseline optically pumped CO–Ar plasma increases the electron density and the ionization fraction by more than an order of magnitude (up to ne=0.9×1010 cm−3 and ne/N=0.8×10−8, respectively), while the gas temperature remains nearly constant, within 3%–5%. Therefore this approach allows varying the electron density in the plasma nearly independently of the gas temperature. The PAD measurements show considerable apparent weakening and dispersion of a shock wave propagating in the optically pumped plasma with a strong radial temperature gradient, compared to the shock propagating in a cold nonionized gas. However, varying the electron density independently of the gas temperature does not produce any detectable effect on the measured gas density distribution across the propagating shock. It is therefore concluded that the observed shock weakening is entirely due to the radial temperature gradient sustained by resonance absorption of the CO laser radiation near the centerline of the shock tube and is not affected by the presence of the charged species in the plasma. © 2002 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1435829
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  • 3
    Electronic Resource
    Electronic Resource
    Radio frequency energy coupling to high-pressure optically pumped nonequilibrium plasmas (2001)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 89 (2001), S. 5911-5918 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: This article presents an experimental demonstration of a high-pressure unconditionally stable nonequilibrium molecular plasma sustained by a combination of a continuous wave CO laser and a sub-breakdown radio frequency (rf) electric field. The plasma is sustained in a CO/N2 mixture containing trace amounts of NO or O2 at pressures of P=0.4–1.2 atm. The initial ionization of the gases is produced by an associative ionization mechanism in collisions of two CO molecules excited to high vibrational levels by resonance absorption of the CO laser radiation with subsequent vibration-vibration (V-V) pumping. Further vibrational excitation of both CO and N2 is produced by free electrons heated by the applied rf field, which in turn produces additional ionization of these species by the associative ionization mechanism. In the present experiments, the reduced electric field, E/N, is sufficiently low to preclude field-induced electron impact ionization. Unconditional stability of the resultant cold molecular plasma is enabled by the negative feedback between gas heating and the associative ionization rate. Trace amounts of nitric oxide or oxygen added to the baseline CO/N2 gas mixture considerably reduce the electron–ion dissociative recombination rate and thereby significantly increase the initial electron density. This allows triggering of the rf power coupling to the vibrational energy modes of the gas mixture. Vibrational level populations of CO and N2 are monitored by infrared emission spectroscopy and spontaneous Raman spectroscopy. The experiments demonstrate that the use of a sub-breakdown rf field in addition to the CO laser allows an increase of the plasma volume by about an order of magnitude. Also, CO infrared emission spectra show that with the rf voltage turned on the number of vibrationally excited CO molecules along the line of sight increase by a factor of 3–7. Finally, spontaneous Raman spectra of N2 show that with the rf voltage the vibrational temperature of nitrogen increases by up to 30%. This novel energy efficient approach allows sustaining large-volume high-pressure molecular plasmas without the use of a high-power CO laser. This opens a possibility of using the present technique for high-yield plasma chemical synthesis and plasma material processing. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1359755
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  • 4
    Electronic Resource
    Electronic Resource
    Phylogenetic analysis of the RNA polymerases of Trypanosoma brucei, with special reference to class-specific transcription (1990)
    Springer
    Current genetics 18 (1990), S. 547-551 
    Details
    ISSN: 1432-0983
    Keywords: Trypanosomes ; RNA polymerase ; Transcription ; Evolution ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have sequenced the genes encoding te largest subunits of the three classes of DNA-dependent RNA polymerases of Trypanosoma brucei. The nucleotide and deduced amino acid sequences were compared and aligned with the corresponding sequences of other eukaryotes. Phylogenetic relationships were subsequently calculated with a distant matrix, a bootstrapped parsimony and a maximum-likelihood method. These independent calculations resulted in trees with very similar topologies. The analyses show that all the largest subunits of T. brucei are evolutionarily distant members within each of the three RNA polymerase classes. An early separation of the trypanosomal subunits from the eukaryotic lineage might from the fundamental basis for the unusual transcription process of this species. Finally, all dendrograms show a separate ramification for the largest subunit of RNA polymerase I, II and III. RNA polymerase II and/or III form a bifurcation with the archaebacterial lineage. RNA polymerase I, however, arises separately from the eubacterial β′ lineage. This suggests that the three eukaryotic RNA polymerase classes are not simply derived by two gene duplications of an ancestral gene with subsequent differentiation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00327026
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  • 5
    Electronic Resource
    Electronic Resource
    The Archaea Monophyly Issue: A Phylogeny of Translational Elongation Factor G(2) Sequences Inferred from an Optimized Selection of Alignment Positions (1999)
    Springer
    Journal of molecular evolution 49 (1999), S. 524-537 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Elongation factor G(2) — BLAST/FASTA — Sequence alignment — Insertion elements — Phylogeny — Archaea — Protein evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. A global alignment of EF-G(2) sequences was corrected by reference to protein structure. The selection of characters eligible for construction of phylogenetic trees was optimized by searching for regions arising from the artifactual matching of sequence segments unique to different phylogenetic domains. The spurious matchings were identified by comparing all sections of the global alignment with a comprehensive inventory of significant binary alignments obtained by BLAST probing of the DNA and protein databases with representative EF-G(2) sequences. In three discrete alignment blocks (one in domain II and two in domain IV), the alignment of the bacterial sequences with those of Archaea–Eucarya was not retrieved by database probing with EF-G(2) sequences, and no EF-G homologue of the EF-2 sequence segments was detected by using partial EF-G(2) sequences as probes in BLAST/FASTA searches. The two domain IV regions (one of which comprises the ADP-ribosylatable site of EF-2) are almost certainly due to the artifactual alignment of insertion segments that are unique to Bacteria and to Archaea–Eucarya. Phylogenetic trees have been constructed from the global alignment after deselecting positions encompassing the unretrieved, spuriously aligned regions, as well as positions arising from misalignment of the G′ and G″ subdomain insertion segments flanking the ``fifth'' consensus motif of the G domain (Ævarsson, 1995). The results show inconsistencies between trees inferred by alternative methods and alternative (DNA and protein) data sets with regard to Archaea being a monophyletic or paraphyletic grouping. Both maximum-likelihood and maximum-parsimony methods do not allow discrimination (by log-likelihood difference and difference in number of inferred substitutions) between the conflicting (monophyletic vs. paraphyletic Archaea) topologies. No specific EF-2 insertions (or terminal accretions) supporting a crenarchaeal–eucaryal clade are detectable in the new EF-G(2) sequence alignment.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006574
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  • 6
    Electronic Resource
    Electronic Resource
    Nucleotide sequence of a DNA region comprising the gene for elongation factor 1α (EF-1α) from the ultrathermophilic archaeotePyrococcus woesei: Phylogenetic implications (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 332-342 
    Details
    ISSN: 1432-1432
    Keywords: Elongation factor ; Archaea ; Phylogeny ; S10 protein ; Pyrococcus woesei
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The gene encoding elongation factor 1α (EF-1α, 1290 bp) of the ultrathermophilic, sulfur-reducing archaeotePyrococcus woesei was localized within aBglII fragment of chromosomal DNA. Sequence analysis showed that the EF-1α gene is the upstream unit of a three-gene cluster comprising the genes for ribosomal protein S10 (306 bp) and transfer RNAser (GGA). The three genes follow each other immediately in the order EF-1α·S10·tRNAser after a putative promoter located 55 bp upstream of the EF-1α gene. Alignment of the derived EF-1α sequence with the corresponding sequences from Eukarya, Bacteria/organelles, and with available archaeal sequences (Sulfolobus, Thermococcus, Methanococcus, Halobacterium) showed thatPyrococcus EF-1α is highly homologous (89% identity) toThermococcus celer EF-1α, both being strikingly more similar to eukaryotic EF-1α than to bacterial EF-Tu. Unrooted dendrograms computed from aligned sequences by distance matrix and DNA parsimony methods, including evolutionary parsimony, showed the Archaea to be a monophyletic-holophyletic cluster closer to Eukarya than to Bacteria. Both distance matrix and DNA parsimony-although not evolutionary parsimony-support the partition of the known archaeal lineages between the kingdoms Crenarchaeota and Euryarchaeota, and the affiliation of thePyrococcus-Thermococcus lineage to the Euryarchaeota, of which it is the most primitive offspring. A closer relation ofPyrococcus to Euryarchaeota than to Crenarchaeota was also inferred from sequence analysis of S10 ribosomal proteins.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02102864
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  • 7
    Electronic Resource
    Electronic Resource
    Early evolutionary relationships among known life forms inferred from elongation factor EF-2/EF-G sequences: Phylogenetic coherence and structure of the archaeal domain (1992)
    Springer
    Journal of molecular evolution 34 (1992), S. 396-405 
    Details
    ISSN: 1432-1432
    Keywords: Phylogeny ; Archaea ; EF-2/EF-G ; Bootstrap ; Monophyly
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Phylogenies were inferred from both the gene and the protein sequences of the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria). All treeing methods used (distance-matrix, maximum likelihood, and parsimony), including evolutionary parsimony, support the archaeal tree and disprove the “eocyte tree” (i.e., the polyphyly and paraphyly of the Archaea). Distance-matrix trees derived from both the amino acid and the DNA sequence alignments (first and second codon positions) showed the Archaea to be a monophyletia-holophyletic grouping whose deepest bifurcation divides a Sulfolobus branch from a branch comprising Methanococcus, Halobacterium, and Thermoplasma. Bootstrapped distance-matrix treeing confirmed the monophyly-holophyly of Archaea in 100% of the samples and supported the bifurcation of Archaea into a Sulfolobus branch and a methanogen-halophile branch in 97% of the samples. Similar phylogenies were inferred by maximum likelihood and by maximum (protein and DNA) parsimony. DNA parsimony trees essentially identical to those inferred from first and second codon positions were derived from alternative DNA data sets comprising either the first or the second position of each codon. Bootstrapped DNA parsimony supported the monophyly-holophyly of Archaea in 100% of the bootstrap samples and confirmed the division of Archaea into a Sulfolobus branch and a methanogen-halophile branch in 93% of the bootstrap samples. Distance-matrix and maximum likelihood treeing under the constraint that branch lengths must be consistent with a molecular clock placed the root of the universal tree between the Bacteria and the bifurcation of Archaea and Eukarya. The results support the division of Archaea into the kingdoms Crenarchaeota (corresponding to the Sulfolobus branch and Euryarchaeota). This division was not confirmed by evolutionary parsimony, which identified Halobacterium rather than Sulfolobus as the deepest offspring within the Archaea.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00162996
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  • 8
    Electronic Resource
    Electronic Resource
    Isolate B12, which harbours a virus-like element, represents a new species of the archaebacterial genus Sulfolobus, Sulfolobus shibatae, sp. nov. (1990)
    Springer
    Archives of microbiology 154 (1990), S. 594-599 
    Details
    ISSN: 1432-072X
    Keywords: Sulfolobus isolate B12 ; Archaebacterial taxonomy ; G+C content ; Sulphur oxidation ; DNA-DNA hybridisation ; 16S rRNA sequence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The Sulfolobus isolate B12 and its endogenous virus-like element SSV1 have provided a fruitful system for detailed analysis of certain aspects of archaebacterial molecular biology, especially those concerning gene expression. In the course of clarifying this isolate's taxonomic position, we determined DNA base composition, ability to grow autotrophically, nucleotide sequence of 16S ribosomal RNA, and level of total genomic homology to other Sulfolobus strains. Although the results generally demonstrate a similarity to S. solfataricus, DNA-DNA hybridisation and 16S rRNA sequence data indicate that isolate B12 in fact represents a distinct species.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00248842
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  • 9
    Electronic Resource
    Electronic Resource
    Gene expression in archaebacteria: Physical mapping of constitutive and UV-inducible transcripts from the Sulfolobus virus-like particle SSV1 (1987)
    Springer
    Molecular genetics and genomics 209 (1987), S. 270-275 
    Details
    ISSN: 1617-4623
    Keywords: Archaebacteria ; Sulfolobus ; Virus transcription ; Promoter ; UV inducibility
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The transcription of the genome of the UV-inducible Sulfolobus virus-like particle SSV1 was studied. Eight different transcripts could be distinguished by Northern analysis that were present in uninduced cells and that coordinately increased in amount after UV induction of SSV1. Using single-stranded DNA probes from different parts of the genome, the approximate map positions of these RNAs and the directions of transcription were determined. In two cases, terminator read-through resulted in the formation of more than one RNA species from a single 5′ end and therefore the eight different RNAs corresponded to only five different transcriptional starts. Two RNAs sharing a common 5′ end encode SSV1 structural proteins. The 5′ end of these transcripts was determined by S1 nuclease analysis. About 20 nucleotides upstream of the transcriptional start of these RNAs, there is an AT-rich region resembling putative promoter sequences which have been found at a similar distance 5′ to the genes encoding stable RNAs in Thermoproteus. In addition to the eight constitutive transcripts, a UV-inducible RNA of 0.3 kb was mapped on the SSV1 genome. In contrast to all other RNAs, it was not detectable in uninduced cells and it is expressed shortly before the amplification and packaging of the SSV1 genome commences.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00329653
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  • 10
    Electronic Resource
    Electronic Resource
    Identification and characterization of a defective SSV1 genome integrated into a tRNA gene in the archaebacterium Sulfolobus sp. B12 (1990)
    Springer
    Molecular genetics and genomics 221 (1990), S. 65-71 
    Details
    ISSN: 1617-4623
    Keywords: Defective virus ; Site-specific integration ; Archaebacterium ; Transfer RNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Within the chromosome of the archaebacterium Sulfolobus sp. B12, a 7.4 kb region was identified which displayed extensive sequence similarities to the 15.5 kb genetic element SSV1 carried by the same strain both as a circular form and as a site-specifically integrated copy. DNA sequence analysis indicated that this 7.4 kb region (designated SSV1intB) represented an SSV1-like element distinguishable from the full-length integrated copy (designated SSV1intA) by extensive deletions and point mutations. The physical organization of DNA sequences of SSV1intB indicated that this element was integrated at the same attP site as previously identified for SSV1intA. A comparison of the DNA sequences at the left attachment sites of SSV1intA and SSV1intB revealed that they both represented very similar putative arginine tRNA genes followed by a 10 by inverted repeat sequence. S1 nuclease mapping experiments indicated that these tRNA genes are transcribed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00280369
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