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  • Life and Medical Sciences  (7)
  • Atomic, Molecular and Optical Physics  (5)
  • in situ hybridization  (5)
  • 2020-2023
  • 1995-1999  (17)
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  • 1
    ISSN: 1573-5028
    Keywords: Beta procumbens ; Beta vulgaris ; in situ hybridization ; repetitive DNA ; satellite DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Members of three prominent DNA families of Beta procumbens have been isolated as Sau3A repeats. Two families consisting of repeats of about 158 bp and 312 bp are organized as satellite DNAs (Sau3A satellites I and II), whereas the third family with a repeat length of 202 bp is interspersed throughout the genome. Multi-colour fluorescence in situ hybridization was used for physical mapping of the DNA families, and has shown that these tandemly organized families occur in large heterochromatic and DAPI positive blocks. The Sau3A satellite I hybridized exclusively around or near the centromeres of 10, 11 or 12 chromosomes. The Sau3A satellite family I showed high intraspecific variability and high-resolution physical mapping was performed on pachytene chromosomes using differentially labelled repeats. The physical order of satellite subfamily arrays along a chromosome was visualized and provided evidence that large arrays of plant satellite repeats are not contiguous and consist of distinct subfamily domains. Re-hybridization of a heterologous rRNA probe to mitotic metaphase chromosomes revealed that the 18S-5.8S-25S rRNA genes are located at subterminal position on one chromosome pair missing repeat clusters of the Sau3A satellite family I. It is known that arrays of Sau3A satellite I repeats are tightly linked to a nematode (Heterodera schachtii) resistance gene and our results show that the gene might be located close to the centromere. Large arrays of the Sau3A satellite II were found in centromeric regions of 16 chromosomes and, in addition, a considerable interspersion of repeats over all chromosomes was observed. The family of interspersed 202 bp repeats is uniformly distributed over all chromosomes and largely excluded from the rRNA gene cluster but shows local amplification in some regions. Southern hybridization has shown that all three families are specific for genomes of the section Procumbentes of the genus Beta.
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  • 2
    ISSN: 1573-5028
    Keywords: Arabidopsis thaliana ; ferns ; in situ hybridization ; phylogenetics ; pines ; reverse transcriptase genes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have investigated the physical distribution of the reverse transcriptase genes of Ty1-copia-like retrotransposable elements from 12 plant species belonging to different subdivisions by hybridization in situ on chromosome preparations. Ty1-copia-like elements showed different and non-random hybridization patterns. A dispersed distribution throughout most of the chromosomes with reduced hybridization at some regions or with some weak clustering at other regions was found in Allium cepa, Beta vulgaris, Brassica campestris, Brassica oleracea, Pennisetum glaucum, Pinus elliottii, Selaginella apoda, Vicia faba and Vicia narbonensis. Reduced hybridization occured mainly at centromeric regions, nucleolus-organizing regions and regions known to be mainly composed of tandemly repeated sequences. In the fern Pteris cretica the retroelements showed a dispersed genomic organization with clustering at some chromosomal regions and whole chromosomes showing little signal. In Arabidopsis thaliana and Cicer arietinum, Ty1-copia-like elements were found in clusters at the paracentromeric heterochromatin, a novel organization for a repetitive element in A. thaliana. New retroelement families were isolated from A. thaliana and from Beta vulgaris. Alignment of the deduced peptide sequences with Ty1-copia-like elements from other plants showed considerable divergence which was used to calculate their relationships, indicating the value of reverse transcriptase gene analysis in phylogenetic and biodiversity studies.
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  • 3
    ISSN: 1573-5028
    Keywords: Arabidopsis arenosa ; Cruciferae ; genus Arabidopsis ; in situ hybridization ; molecular systematics ; satellite DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have analysed a family of highly repetitive DNA from Arabidopsis arenosa (L.) Lawalrée [syn. Cardaminopsis arenosa (L.) Hayck] composed of AT-rich tandem repeats of 166–179 bp in head to tail organization. Sequence comparison between several repeat units revealed a high level of divergence of 4.5% to 25%. The sequence family shows more than 58% homology to satellite sequences described in Arabidopsis thallana (L.) Heynh. but no homology to other satellite repeats in the Cruciferae. Within the genus Arabidopsis the satellite sequence was found to be present in A. thaliana and Arabidopsis suecica (Fries) Norrlin, but not in Arabidopsis griffithiana (Boiss.) N. Busch and Arabidopsis pumila (Stephan) N. Busch. In situ hybridization to metaphase chromosomes of A. arenosa (2n=4x=32) showed the sequence to be localized at the centromeres of all 32 chromosomes with substantial hybridization along the chromosome arms. Using Southern hybridization and in situ hybridization, we give evidence that A. suecica is a hybrid of A. thaliana and A. arenosa. A considerable reorganization of the A. thaliana satellite sequence pAL1 occurred in the hybrid genome while no molecular change of the A. arenosa repeat was observed in the hybrid. Analysis of related repeats enabled differentiation between closely related genomes and are useful for the investigation of hybrid genomes.
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  • 4
    ISSN: 1573-6849
    Keywords: Beta vulgaris ; in situ hybridization ; LINE ; LTR retrotransposons ; non-LTR (non-viral) retrotransposons ; Ty1-copia
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract DNA sequences of the reverse transcriptase gene of long terminal repeat (LTR) and non-LTR (non-viral) retrotransposons have been isolated and cloned from the genome of sugar beet (Beta vulgaris). Both retrotransposon types are highly amplified in sugar beet and may account for 2–5% of the genome. The BNR1 family, representing the first non-viral retrotransposon reported from a dicotyledonous species, shows homology to the mammalian L1 family of long interspersed repeated sequences (LINEs) and to retrotransposable elements from maize and lily. Sequences of the Tbv family are homologous to theTy1-copia class of LTR retrotransposons. The BNR1 and Tbv retrotransposon families are characterized by sequence heterogeneity and are probably defective. The deduced peptide sequences were used to investigate the relation to other retroelements from plants, insects and mammals. Fluorescencein situ hybridization was used to investigate the physical distribution and revealed that both retrotransposon families are present on all sugar beet chromosomes and largely excluded from chromosomal regions harbouring the 18S–5.8S–25S rRNA genes. The BNR1 family is organized in discrete clusters, while the Tbv family ofTy1-copia-like retrotransposons shows a more uniform distribution along chromosome arms and is absent from some chromosomal regions. These contrasting distributions emphasize the differences in evolutionary amplification and dispersion mechanisms between the two types of retrotransposons. Thein situ results of both elements reflect significant features of a higher order structure of the genome, as it is known for both short interspersed repeated sequences (SINEs) and LINEs in human.
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  • 5
    ISSN: 1573-5028
    Keywords: sugar beet (Beta vulgaris) ; LINEs ; non-LTR retrotransposons ; reverse transcriptase gene ; in situ hybridization ; genome organization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have isolated and characterized conserved regions of the reverse transcriptase gene from non-LTR retrotransposons, also called long interspersed nuclear elements (LINEs), from Beta vulgaris, B. lomatogona and B. nana. The novel elements show strong homology to other non-LTR retrotransposons from plants, man and animals. LINEs are present in all species of the genus Beta tested, but there was variation in copy number. Analysis by Southern hybridization and fluorescent in situ hybridization revealed the clustered organization of these retroelements in beet species. PCR amplification using degenerate primers to conserved motifs of the predicted LINE protein sequence enabled the cloning of LINEs from both Monocotyledonae (Allium cepa, Oryza sativa and Secale cereale) and Dicotyledonae (Nicotiana tabacum and Antirrhinum majus) indicating that LINEs are a universal feature of plant genomes. A dendrogram of fifteen new and six previously isolated sequences showed the high level of sequence divergence while revealing families characteristic of some genera. The genomic organization of non-LTR retrotransposons was examined more detailed in A. majus and O. sativa.
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 53 (1995), S. 635-649 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The subject of this article is the self-consistent-field (SCF) treatment of low-lying molecular vibrations in molecules subject to solvent effects and light atom migration. The analyses use a Cartesian Gaussian basis and Gaussian functional expansions of potential energy operators. The objective of the work was to establish approximate and practical methods of analysis of vibrational degrees of freedom in molecules that build on and compare well with the highly accurate treatments of vibrations in small molecular systems of the past decade. An application to a system in which hydrogen bonding contributes the major anharmonic effect illustrates the method. © 1995 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 53 (1995), S. 663-677 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This article presents methods for computing matrix elements with Cartesian Gaussian wave functions of potential energy operators that depend on functions of the form (r-r0)n exp[-a(r - r0)] as well as matrix elements of the class of polynomial many-body potentials developed by Murrell et al. The matrix elements arise in the analyses of anharmonic vibrations in molecules. © 1995 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 56 (1995), S. 203-206 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ab initio calculation of periodically Si-δ-doped GaAs was performed in the regime of high-donor concentration. The electronic confinement exhibit a quasi-2D behavior even for small periods (p = 45 Å). The electronic properties of the clustering SiGa—SAs also was studied. © 1995 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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  • 9
    ISSN: 0730-2312
    Keywords: cancer ; chemoprevention ; clinical trial ; surrogate endpoint biomarker ; protocol design ; safety ; efficacy ; FDA ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: As with other drugs, applications for marketing approval of new chemopreventive agents in the United States must include data from adequate and well-controlled clinical trials that demonstrate effectiveness and safety for the intended use. Knowledge of a drug's pharmacologic actions and metabolism may benefit protocol design, by identifying the patient populations and dosing schedules associated with a favorable risk/benefit profile. With availability of appropriate preclinical data, including standard assessments of an agent's toxicology, effects on reproductive performance, and genotoxicity, initial Phase I studies of 1-3 months may be performed in normal volunteers or an appropriate higher-risk population. For chronic dosing studies of longer duration, preclinical toxicology studies of longer duration are relevant. Enrollment in chemoprevention studies should be directed toward individuals at sufficient risk of developing cancer so that potential benefit may counterbalance the unpredictable and possibly serious adverse effects that may be observed with prolonged administration of a study drug. Phase I and II studies with clinical dosing lasting up to 12 months often afford opportunities to assess drug effect on surrogate endpoint biomarkers that may correlate with endpoints of clinical effectiveness. Phase III and late phase II chemopreventive investigations should routinely utilize a prospective, randomized study design (double-masked and placebo-controlled, when possible). To support marketing approval, there must be evidence that a chemopreventive agent significantly delays or prevents the occurrence of malignancy, with acceptable safety. In some circumstances, modulation of a surrogate marker may provide a basis for marketing approval, before more definitive endpoint data become available. However, the acceptability of a surrogate depends on the nature and quality of the data supporting its predictive value. Given the considerations of large study size, long duration, and high cost that may hamper development of potential agents, studies designed to examine the predictive value of surrogate endpoint biomarkers are of great importance to the future development of chemoprevention research. J. Cell. Biochem. Suppl. 27:1-6. Published 1998 Wiley-Liss, Inc.
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 53 (1995), S. 651-661 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This article presents methods for computing Cartesian Gaussian matrix elements using a Taylor series for general potential energy operators that admit well-behaved radial derivatives. These operators arise in the analyses of anharmonic vibrations in molecules. Application to the evaluation of matrix elements for hydrogen associated two wells illustrates the method. © 1995 John Wiley & Sons, Inc.
    Additional Material: 2 Tab.
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