ALBERT — All Library Books, journals and Electronic Records Telegrafenberg

1

Electronic Resource

Meiotic recombination in RAD54 mutants of Saccharomyces cerevisiae (2000)

Schmuckli-Maurer, Jacqueline ; Heyer, Wolf-Dietrich

Springer

Chromosoma 109 (2000), S. 86-93

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ISSN: 1432-0886

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Medicine

Notes: Abstract. The Rad54 protein is an important component of the recombinational DNA repair pathway in vegetative Saccharomyces cerevisiae cells. Unlike those in other members of the RAD52 group, the meiotic defect in rad54 is rather mild, reducing spore viability only to 26%–65%. A consistently greater requirement for Rad54p during meiosis was observed in hybrid strains, suggesting that Rad54p has a certain role in interhomolog interactions. Such a role is probably minor as no recombination defects were found in the surviving gametes in three genetic intervals on chromosome V. Also, the spore viability pattern in tetrads did not reflect an increase in nondisjunction at meiosis I indicative of a meiotic recombination defect. We suggest that the meiotic defect of rad54 cells lies in the failure to repair meiosis-specific double-strand breaks outside the context of the highly differentiated pathway leading to interhomolog joint molecules and meiotic crossovers that ensure accurate segregation at meiosis I.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s004120050415

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2

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Activity and community structure of methane-oxidising bacteria in a wet meadow soil (2002)

Horz, Hans-Peter ; Raghubanshi, Akhilesh S. ; Heyer, Jürgen ; [et al.]

Oxford, UK : Blackwell Publishing Ltd

FEMS microbiology ecology 41 (2002), S. 0

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ISSN: 1574-6941

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: The structure and activity of the methane-oxidising microbial community in a wet meadow soil in Germany were investigated using biogeochemical, cultivation, and molecular fingerprinting techniques. Both methane from the atmosphere and methane produced in anaerobic subsurface soil were oxidised. The specific affinity (first-order rate constant) for methane consumption was highest in the top 20 cm of soil and the apparent half-saturation constant was 137–300 nM CH4, a value intermediate to measured values in wetland soils versus well-aerated upland soils. Most-probable-number (MPN) counting of methane-oxidising bacteria followed by isolation and characterisation of strains from the highest positive dilution steps suggested that the most abundant member of the methane-oxidising community was a Methylocystis strain (105–107 cells g−1 d.w. soil). Calculations based on kinetic data suggested that this cell density was sufficient to account for the observed methane oxidation activity in the soil. DNA extraction directly from the same soil samples, followed by PCR amplification and comparative sequence analyses of the pmoA gene, also detected Methylocystis. However, molecular community fingerprinting analyses revealed a more diverse and dynamic picture of the methane-oxidising community. Retrieved pmoA sequences included, besides those closely related to Methylocystis spp., others related to the genera Methylomicrobium and Methylocapsa, and there were differences across samples which were not evident in MPN analyses.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1111/j.1574-6941.2002.tb00986.x

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3

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Isolation of a Methylocystis strain containing a novel pmoA-like gene (2002)

Dunfield, Peter F. ; Yimga, Merlin Tchawa ; Dedysh, Svetlana N. ; [et al.]

Oxford, UK : Blackwell Publishing Ltd

FEMS microbiology ecology 41 (2002), S. 0

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ISSN: 1574-6941

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: A type II methanotrophic bacterium (Methylocystis strain SC2) was isolated from a polluted aquifer and identified based on morphology and on 16S rRNA gene phylogeny. Primers targeting the particulate methane monooxygenase subunit A gene (pmoA) were used to obtain a PCR product from DNA extract of strain SC2. Denaturing gradient gel electrophoresis of this PCR product demonstrated that strain SC2 contained two very different pmoA-like genes. One gene (pmoA1) had very high sequence homology to pmoA genes of other type II methanotrophic bacteria (identical amino acid sequence to pmoA of some other Methylocystis strains). The second gene (pmoA2) possessed only 73% identity with the first gene at the nucleotide level and 68.5% identity (83% similarity) at the amino acid level. The presence of both pmoA-like genes was verified by developing specific oligonucleotide probes for each and using these in Southern hybridisation of genomic DNA. Purity of the culture was exhaustively verified with a variety of methods to ensure that both genes were present in a single genospecies. These included microscopic examination, plating on various media, denaturing gradient gel electrophoresis of PCR products of the 16S rRNA gene (universal to bacteria) and of the methanol dehydrogenase α-subunit gene mxaF (universal to methylotrophic bacteria), and whole-cell hybridisation with fluorescently labelled 16S rRNA-targeted oligonucleotide probes specific for the genera Methylosinus and Methylocystis, or specific for strain SC2. Reverse transcription PCR of extracted RNA suggested that the novel pmoA2 gene was not expressed during growth under standard conditions used for the cultivation of these bacteria. The presence of multiple, diverse pmoA-like genes in a single genospecies of methanotrophic bacteria implies that pmoA must be cautiously applied as a phylogenetic marker in cultivation-independent molecular ecology studies.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1111/j.1574-6941.2002.tb00962.x

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4

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Impact of soluble sugar concentrations on the acquisition of freezing tolerance in accessions of Arabidopsis thaliana with contrasting cold adaptation – evidence for a role of raffinose in cold acclimation (2004)

KLOTKE, J. ; KOPKA, J. ; GATZKE, N. ; [et al.]

Oxford, UK : Blackwell Science Ltd

Plant, cell & environment 27 (2004), S. 0

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ISSN: 1365-3040

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: In the present study the cold acclimation potential of two accessions of Arabidopsis thaliana was investigated. Significant variation was found for basic tolerance as well as the capacity to acclimate to freezing temperatures. During cold acclimation, levels of soluble sugars increased in both genotypes, but raffinose accumulation discriminated the more tolerant accession Col-0 from C24. Concentrations of other compatible solutes such as proline and glutamine were also higher in cold-acclimated Col-0 than C24 plants. Changes of invertase activity during cold exposure corresponded to changes in sucrose and fructose, but not glucose concentrations and were consistent with an initial chilling response and a later decline in hexose metabolization. When vacuolar invertase was suppressed by siRNA expression, reduced sucrolytic activity resulted in elevated leaf sucrose concentration, whereas the fructose content was strongly reduced. This led to elevated freezing tolerance in the cold-tolerant genotype Col-0, but not in C24. The most pronounced metabolic changes in invertase-inhibited Col-0 plants occurred for proline and glutamine concentrations, indicating indirect metabolic effects of altered sugar concentrations.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1111/j.1365-3040.2004.01242.x

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5

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Differential detection of type II methanotrophic bacteria in acidic peatlands using newly developed 16S rRNA-targeted fluorescent oligonucleotide probes (2003)

Dedysh, Svetlana N ; Dunfield, Peter F ; Derakshani, Manigee ; [et al.]

Oxford, UK : Blackwell Publishing Ltd

FEMS microbiology ecology 43 (2003), S. 0

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ISSN: 1574-6941

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: Based on an extensive 16S rRNA sequence database for type II methanotrophic bacteria, a set of 16S rRNA-targeted oligonucleotide probes was developed for differential detection of specific phylogenetic groups of these bacteria by fluorescence in situ hybridisation (FISH). This set of oligonucleotides included a genus-specific probe for Methylocystis (Mcyst-1432) and three species-specific probes for Methylosinus sporium (Msins-647), Methylosinus trichosporium (Msint-1268) and the recently described acidophilic methanotroph Methylocapsa acidiphila (Mcaps-1032). These novel probes were applied to further characterise the type II methanotroph community that was detected in an acidic Sphagnum peat from West Siberia in a previous study (Dedysh et al. (2001) Appl. Environ. Microbiol. 67, 4850–4857). The largest detectable population of indigenous methanotrophs simultaneously hybridised with a group-specific probe targeting all currently known Methylosinus/Methylocystis spp. (M-450), with a genus-specific probe for Methylocystis spp. (Mcyst-1432), and with an additional probe (Mcyst-1261) that had been designed to target a defined phylogenetic subgroup of Methylocystis spp. The same subgroup of Methylocystis was also detected in acidic peat sampled from Sphagnum-dominated wetland in northern Germany. The population size of this peat-inhabiting Methylocystis subgroup was 2.0±0.1×106 cells g−1 (wet weight) of peat from Siberia and 5.5±0.5×106 cells g−1 of peat from northern Germany. This represented 60 and 95%, respectively, of the total number of methanotroph cells detected by FISH in these two wetland sites. Other major methanotroph populations were M. acidiphila and Methylocella palustris. Type I methanotrophs accounted for not more than 1% of total methanotroph cells. Neither M. trichosporium nor M. sporium were detected in acidic Sphagnum peat.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1111/j.1574-6941.2003.tb01070.x

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6

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MUS81 encodes a novel Helix-hairpin-Helix protein involved in the response to UV- and methylation-induced DNA damage in Saccharomyces cerevisiae (2000)

Interthal, H. ; Heyer, W.-D.

Springer

Molecular genetics and genomics 263 (2000), S. 812-827

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ISSN: 1617-4623

Keywords: Key words DNA repair ; Helix-hairpin-Helix motif ; Methylmethane sulfonate (MMS) ; Saccharomyces cerevisiae ; UV radiation

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract The gene MUS81 (Methyl methansulfonate, UV sensitive) was identified as clone 81 in a two-hybrid screen using the Saccharomyces cerevisiae Rad54 protein as a bait. It encodes a novel protein with a predicted molecular mass of 72,316 (632 amino acids) and contains two helix-hairpin-helix motifs, which are found in many proteins involved in DNA metabolism in bacteria, yeast, and mammals. Mus81p also shares homology with motifs found in the XPF endonuclease superfamily. Deletion of MUS81 caused a recessive methyl methansulfonate- and UV-sensitive phenotype. However, mus81Δ cells were not significantly more sensitive than wild-type to γ-radiation or double-strand breaks induced by HO endonuclease. Double mutant analysis suggests that Rad54p and Mus81p act in one pathway for the repair of, or tolerance to, UV-induced DNA damage. A complex containing Mus81p and Rad54p was identified in immunoprecipitation experiments. Deletion of MUS81 virtually eliminated sporulation in one strain background and reduced sporulation and spore viability in another. Potential homologs of Mus81p have been identified in Schizosaccharomyces pombe, Caenorhabditis elegans and Arabidopsis thaliana. We hypothesize that Mus81p plays a role in the recognition and/or processing of certain types of DNA damage (caused by UV and MMS) during repair or tolerance processes involving the recombinational repair pathway.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s004380000241

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7

Electronic Resource

Cartilage Cultivation on a Calcium Phosphate Ceramic in a Bioreactor System (2004)

Nagel-Heyer, S. ; Janssen, Rolf ; Goepfert, C. ; [et al.]

s.l. ; Stafa-Zurich, Switzerland

Key engineering materials Vol. 264-268 (May 2004), p. 2119-2122

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ISSN: 1013-9826

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

Type of Medium: Electronic Resource

URL: http://www.tib-hannover.de/fulltexts/2011/0528/01/48/transtech_doi~10.4028%252Fwww.scientific.net%252FKEM.264-268.2119.pdf

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8

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A Generalized Erdös-Rényi Law for Sequence Analysis Problems (2000)

Heyer, Laurie J.

Springer

Methodology and computing in applied probability 2 (2000), S. 309-329

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ISSN: 1387-5841

Keywords: strong law ; Erdös-Rényi law ; sequence analysis ; alignment ; structural alignment

Source: Springer Online Journal Archives 1860-2000

Topics: Mathematics

Notes: Abstract We consider a class of random variables that includes scoring functions arising in computational molecular biology, such as sequence alignment and folding. We characterize the class by a set of properties, and show that, under certain conditions, such random variables follow an Erdös-Rényi law of large numbers. That is, $$\begin{gathered} _{\text{2}}^{\text{ + }} \hfill \\ \hfill \\ \mathop {\lim }\limits_{n \to \infty } \frac{{T_n }}{{\log n}} = sd{\text{ a}}{\text{.s}}{\text{.}} \hfill \\ \end{gathered} $$ where Tn is the maximum score over contiguous regions from each of s independent sequences, and d is a function of the large deviation rate of the scoring function. This result unifies several others, and applies to more general scoring systems on any number of sequences. We show how the theorem can be applied to a recently introduced scoring function. Finally, we conjecture that a modified form of this function behaves similarly, and support the conjecture with simulations.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1023/A:1010085313469

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9

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A new deal for Holliday junctions (2004)

Heyer, Wolf-Dietrich

[s.l.] : Nature Publishing Group

Nature structural & molecular biology 11 (2004), S. 117-119

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ISSN: 1545-9985

Source: Nature Archives 1869 - 2009

Topics: Biology , Medicine

Notes: [Auszug] Fifty years ago Bloom described a congenital disorder that now bears his name. Since that time, Bloom's syndrome has become a classic example of genomic instability syndromes. Affected humans have significant predisposition for the development of many types of cancer, particularly non-Hodgkins ...

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1038/nsmb0204-117

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