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  • 1
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Science Ltd
    Freshwater biology 48 (2003), S. 0 
    ISSN: 1365-2427
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: 1. Recent research has shown that high-flow events in streams leave a small-scale mosaic of bed patches that have experienced scouring, sediment deposition (fill), or remained stable. Few studies have investigated if this ‘local disturbance history’ contributes to the patchy distribution of benthic organisms in streams and rivers.2. In the present research, we demonstrate that local disturbance history in a mid-sized river can have both short- and long-term effects on epilithic algae. Chains buried vertically in the substratum of the river bed (236 in a 800-m reach) indicated that two floods (return periods ≤1 year) caused a mosaic of bed patches with different disturbance histories. Once after the first and twice after the second flood, we sampled epilithic algae (mainly diatoms) in replicate patches that had been scoured, filled, or remained stable during the respective event. Algal biomass and cell density per substratum area were determined.3. Three months after the first flood, algal biomass, total diatom density, diatom taxon richness, and densities of six of nine most common taxa were highest in fill patches. Six days after the second flood, biomass was highest in stable patches, indicating a refugium function of these patches. The refugium patches consisted of average-sized stones, in contrast to previous studies of flood refugia for benthic algae in which these refugia were always large and/or immobile substrata. Four weeks after the second flood, diatoms tended to be most abundant in scour patches. With one exception, these differences between patch types could not be attributed to differences in local near-bed current velocity or water depth.4. The effects of disturbance history were more complex than a simple refugium function of stable patches because algal patterns changed with time since the last disturbance, possibly depending on the successional state of the algal mats.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: By generating a specialized cDNA library from the archaeon Sulfolobus solfataricus, we have identified 57 novel small non-coding RNA (ncRNA) candidates and confirmed their expression by Northern blot analysis. The majority was found to belong to one of two classes, either antisense or antisense-box RNAs, where the latter only exhibit partial complementarity to RNA targets. The most prominent group of antisense RNAs is transcribed in the opposite orientation to the transposase genes, encoded by insertion elements (transposons). Thus, these antisense RNAs may regulate transposition of insertion elements by inhibiting expression of the transposase mRNA. Surprisingly, the class of antisense RNAs also contained RNAs complementary to tRNAs or sRNAs (small-nucleolar-like RNAs). For the antisense-box ncRNAs, the majority could be assigned to the class of C/D sRNAs, which specify 2′-O-methylation sites on rRNAs or tRNAs. Five C/D sRNAs of this group are predicted to target methylation at six sites in 13 different tRNAs, thus pointing to the widespread role of these sRNA species in tRNA modification in Archaea. Another group of antisense-box RNAs, lacking typical C/D sRNA motifs, was predicted to target the 3′-untranslated regions of certain mRNAs. Furthermore, one of the ncRNAs that does not show antisense elements is transcribed from a repeat unit of a cluster of small regularly spaced repeats in S. solfataricus which is potentially involved in replicon partitioning. In conclusion, this is the first report of stably expressed antisense RNAs in an archaeal species and it raises the prospect that antisense-based mechanisms are also used widely in Archaea to regulate gene expression.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] According to small subunit ribosomal RNA (ss rRNA) sequence comparisons all known Archaea belong to the phyla Crenarchaeota, Euryarchaeota, and—indicated only by environmental DNA sequences—to the ‘Korarchaeota’. Here we report the cultivation of a new ...
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1673-1675 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A group of anaerobic microorganisms use sulfate as the terminal electron acceptor for energy conservation. The process of sulfate reduction involves several enzymatic steps. One of them is the conversion of adenylyl sulfate (adenosine-5′-phosphosulfate) to sulfite, catalyzed by adenylylsulfate reductase. This enzyme is composed of a FAD-containing α-subunit and a β-subunit harbouring two [4Fe–4S] clusters. Adenylylsulfate reductase was isolated from Archaeoglobus fulgidus under anaerobic conditions and crystallized using the hanging-drop vapour-diffusion method using PEG 4000 as precipitant. The crystals grew in space group P212121, with unit-cell parameters a = 72.4, b = 113.2, c = 194.0 Å. The asymmetric unit probably contains two αβ units. The crystals diffract beyond 2 Å resolution and are suitable for X-ray structure analysis.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Extremophiles 2 (1998), S. 101-108 
    ISSN: 1433-4909
    Keywords: Key words Hyperthermophilic archaea ; Genome sizes ; Sulfolobales ; Pulsed field gel electrophoresis ; Thermophilic bacteria ; Phylogenetic analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Genomes of various hyperthermophilic and extremely thermophilic prokaryotes were analyzed with respect to size, physical organization, and 16S rDNA copy number. Our results show that all the genomes are circular, and they are in the size range of 1.6–1.8 Mb for Pyrodictium abyssi, Methanococcus igneus, Pyrobaculum aerophilum, Archaeoglobus fulgidus, Archaeoglobus lithotrophicus, and Archaeoglobus profundus (the two bacteria Fervidobacterium islandicum and Thermosipho africanus possess genomes of 1.5-Mb size). A systematic study of all validly described species of the order Sulfolobales revealed the existence of two classes of genome size for these archaea, correlating with phylogenetic analyses. The Metallosphaera–Acidianus group, plus Sulfolobus metallicus, have genomes of ca. 1.9 Mb; the other members of the order Sulfolobales group possess genomes 〉2.7 Mb. The special case of Stygiolobus azoricus is discussed.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1432-1432
    Keywords: Sulfolobales ; Protein synthesis ; Antibiotics ; Ribosomal function
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The sensitivity of the cell-free protein synthesis systems from Acidanus brierleyi, Acidianus infernus, and Metallosphaera sedula, members of the archaeal order Sulfolobales, to 40 antibiotics with different specificities has been studied. The sensitivity patterns were compared to those of Sulfolobus solfataricus and other archaeal, bacterial, and eukaryotic systems. The comparative analysis shows that ribosomes from the sulfolobales are the most refractory to inhibitors of protein synthesis described so far. The sensitivity results have been used to ascertain in phylogenetic relationships among the members of the order Sulfolobales. The evolutionary significance of these results are analyzed in the context of the phylogenetic position of this group of extreme thermophilic microorganisms.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1432-1432
    Keywords: Archaebacteria ; Taxonomy ; Evolution ; DNA ; 16S rRNA ; Hybridization ; Phylogeny ; Thermoproteales
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary DNAs from 16 species of archaebacteria including 6 novel isolates were hybridized with 16S rRNAs from 7 species representing different orders or groups of the urkingdom of archaebacteria. The yields, normalized for the number of genes perµg of DNA, and the temperature stabilities of all hybrids were determined and related to each other. A taxonomic tree constructed from such fractional stability data reveals the same major divisions as that derived from comparative cataloging of 16S rRNA sequences. The extreme halophiles appear however as a distinct order besides the three known divisions of methanogens. The methanogens, the halophiles andThermoplasma form one of two clearly recognizable branches of the archaebacterial urkingdom. The order represented bySulfolobus and the related novel orderThermoproteales form the other branch. Three novel genera,Thermoproteus, Desulfurococcus and the “stiff filaments” represent three families of this order. The extremely thermophilic methanogenMethanothermus fervidus belongs to theMethanobacteriales. SN1, a methanogen from Italy, appears as another species of the genusMethanococcus. Another novel methanogen, M3, represents a genus or family of the orderMethanomicrobiales.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1662-8985
    Source: Scientific.Net: Materials Science & Technology / Trans Tech Publications Archiv 1984-2008
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: To enhance our understanding of effects of microbially mediated pyrite dissolution and theinfluence parameters such as varied metabolism and crystallographic orientation of pyrite surfacessome dissolution experiments were performed. Microbial etching experiments on pyrite surfaces ofdifferent orientation, including {111} and {210} were devised. The experiments were performedusing two strains of thermophilic Archaea (Sulfolobus metallicus, Metallosphaera sedula).Epifluorescence microscopy observations showed that the strains attach to the mineral surface.Studies with Scanning Electron Microscopy (SEM) showed cell attachment and etching effects afterone week of incubation. Surface alteration produced structures following crystallographicorientation up to several 10 μm in size. For all incubated pyrite samples it became apparent thatsurface alteration was more pronounced with M. sedula than with S. metallicus
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1432-1327
    Keywords: Key words Ferredoxins ; Thermophiles ; Archaea ; EPR ; Iron-sulfur
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  Seven-iron ferredoxins from the thermoacidophilic archaea Acidianus ambivalens, A. infernus, Metalosphaera prunae and Sulfolobus metallicus were extensively characterised, allowing study of their expression under aerobic and anaerobic growth conditions as well as the putative role in thermal stability of a recently described zinc centre. The archaeon S. metallicus was found to express, under the same growth conditions, two ferredoxins in almost identical amounts, a novelty among Archaea. Most interestingly, these two ferredoxins differ at the N-terminal amino acid sequence in that one has a zinc binding motif (FdA) and the other does not (FdB); in agreement with these findings, FdA contains a zinc ion and FdB does not. These two ferredoxins have identical thermal stabilities, indicating that the zinc atom is not determinant in the protein thermostability. Further, the presence of the additional zinc centre does not interfere with the redox properties of the iron-sulfur clusters since their reduction potentials are almost identical. From the other three archaea, independently of the growth mode in respect to oxygen, only a single zinc-containing ferredoxin was found. EPR studies on the purified proteins, both in the oxidised and dithionite reduced states, allowed the identification of one [3Fe-4S]1+/0 centre and one [4Fe-4S]2+/1+ centre in all proteins studied. The complete sequence of A. ambivalens ferredoxin is reported. Together with the data gathered in this study, the properties of the seven-iron ferredoxins from Sulfolobales so far known are re-discussed.
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1432-072X
    Keywords: Thiobacillus ; Leaching ; Chemolithotrophic ; Acidophilic ; Marine
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract From the shallow geothermally heated seafloor at the beach of Porto di Levante (Vulcano, Italy) 8 strains of long, tiny rods were isolated, which represent the first marine metal-mobilizing bacteria. Cells are Gram negative. They grow in a temperature range between 23 and 41°C with an optimum around 37°C at a salt concentration of up to 6.0% NaCl. The isolates are obligately chemolithotrophic, acidophilic aerobes which use sulfidic ores, elemental sulfur or ferrous iron as energy sources and procedure sulfuric acid. They show an upper pH-limit of growth at around 4.5. The G+C content of their DNA is around 64 mol%. Based on the results of the DNA-DNA hybridization they represent a new group within the genus Thiobacillus. Isolate LM3 is described as the type strain of the new species Thiobacillus prosperus.
    Type of Medium: Electronic Resource
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