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  • 2010-2014
  • 1990-1994  (4,401)
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  • 1890-1899
  • Biochemistry and Biotechnology  (4,158)
  • Industrial Chemistry  (1,117)
  • Brassica napus
  • transformation
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Material
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Year
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  • 1
    Electronic Resource
    Electronic Resource
    Plasmid mediated silver resistance in Acinetobacter baumannii (1994)
    Springer
    BioMetals 7 (1994), S. 49-56 
    Details
    ISSN: 1572-8773
    Keywords: Acinetobacter ; conjugation ; curing ; plasmid ; silver uptake ; silver resistance ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Acinetobacter baumannii BL88, an environmental isolate, was resistant to 13 metals and 10 antibiotics. Plumbagin cured resistance to silver, cadmium, antimony, streptomycin and ampicillin at varying frequencies. However, only silver resistance transferred (1 × 10−6 recepient−1) to Escherichia coli K12 during conjugation. Correspondingly there was transfer of a 54 kb plasmid (pUPI199) from A. baumannii BL88. The plasmid transformed E. coli DH5α cells at a frequency of 1 × 10−8 recepient−1. The growth rate of E. coli DH5; (pUPI199) was slower as compared with E. coli DH5α. Plasmid pUPI199 was 76 and 9.6% stable in the host A. baumannii BL88 in the presence and absence of selection pressure, respectively. A. baumannii BL88 was found to accumulate and retain silver whereas E. coli DH5α (pUPI199) effluxed 63% of the accumulated silver ions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00205194
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  • 2
    Electronic Resource
    Electronic Resource
    Canonical correlation and reduction of multiple time series (1994)
    Springer
    Annals of the Institute of Statistical Mathematics 46 (1994), S. 625-631 
    Details
    ISSN: 1572-9052
    Keywords: Rank of multiple time series ; transformation ; spectrum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract It is shown that a degenerate rankd-variate stationary time series can be reduced to a full rank time series of lower dimension via an orthogonal transformationT provided that ρ, the canonical correlation between past and future of the time series is strictly less than one. Procedures for estimation of rank of the multiple time series,T and testing ρ=1 are outlined, the latter is related to testing the unit root hypothesis in ARMA models.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00773471
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  • 3
    Electronic Resource
    Electronic Resource
    Genetic ecology: A new interdisciplinary science, fundamental for evolution, biodiversity and biosafety evaluations (1994)
    Springer
    Cellular and molecular life sciences 50 (1994), S. 429-437 
    Details
    ISSN: 1420-9071
    Keywords: Genetics ; ecology ; DNA-transfer ; conjugation ; transformation ; transduction ; transposons ; dormant cells ; epilithon ; microbial colonisation ; symbiosis ; virus resistance ; biosafety ; release of genes ; insults to humanity ; evolution ; biodiversity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Genetic ecology is the extension of our modern knowledge in molecular genetics to studies of viability, gene expression and gene movements in natural environments like soils, aquifers and digestive tracts. In such milieux, the horizontal transfer of plasmid-borne genes between phylogenetically distant species has already been found to be much more frequent than had been expected from laboratory experience. For the study of exchanges involving chromosomally-located genes, more has to be learned about the behaviour of transposons in such environments. The results expected from studies in genetic ecology are relevant for considerations of evolution, biodiversity and biosafety. The role of this new field of research in restoring popular confidence in science and in its biotechnological applications is stressed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01920741
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  • 4
    Electronic Resource
    Electronic Resource
    Agrobacterium-mediated transformation of white mustard (Sinapis alba L.) and regeneration of transgenic plants (1994)
    Springer
    Plant cell reports 13 (1994), S. 130-134 
    Details
    ISSN: 1432-203X
    Keywords: Sinapis alba L. ; Agrobacterium tumefaciens ; transformation ; regeneration
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A procedure for the regeneration of fertile transgenic white mustard (Sinapis alba L.) is presented. The protocol is based on infection of stem explants of 7–9 day old plants with an Agrobacterium tumefaciens strain harboring a disarmed binary vector with chimeric genes encoding neomycin phosphotransferase and β-glucuronidase. Shoots are regenerated from callus-forming explants within 3–4 weeks. Under selection, 10% of the explants with transgenic embryonic callus develop into fertile transgenic plants. Rooting shoots transferred to soil yield seeds within 14–16 weeks following transformation. Integration and expression of the T-DNA encoded marker genes was confirmed by histochemical β glucuronidase assays and Southern-DNA hybridization using primary transformants and S1-progeny. The analysis showed stable integration and Mendelian inheritance of trans-genes in transformed Sinapis lines.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00239878
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  • 5
    Electronic Resource
    Electronic Resource
    Stable expression of the GUS reporter gene in chrysanthemum depends on binary plasmid T-DNA (1994)
    Springer
    Plant cell reports 14 (1994), S. 59-64 
    Details
    ISSN: 1432-203X
    Keywords: Agrobacterium ; transformation ; T-DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Three chrysanthemum (Dendranthema grandiflora) cultivars were cocultivated with 2 Agrobacterium tumefaciens strains in combination with 4 pBIN19 derived binary plasmids, all carrying the Nosnptll selection gene and 35Sgus(intron) reporter gene. All binary plasmids transferred DNA to chrysanthemum explants but only pMOG410 gave good stable expression of GUS. This plasmid differs from the other plasmids in 2 aspects: 1) It carries a restored nptll gene and 2) the selection gene is positioned at the left border side of the reporter gene. Cocultivation with AGLO(pMOG410) yielded up to 13 GUS positive shoots per 100 explants. The presence of the gus and nptll gene in recovered shoots was confirmed by PCR and Southern blot analysis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00233300
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  • 6
    Electronic Resource
    Electronic Resource
    Isolation and transformation of rice aleurone protoplasts (1994)
    Springer
    Plant cell reports 13 (1994), S. 394-396 
    Details
    ISSN: 1432-203X
    Keywords: Rice ; α-amylase ; protoplasts ; aleurone ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Protoplasts isolated from the aleurone have been used extensively in molecular studies focusing on hormone-mediated regulation of gene expression in barley seed. To extend the use of aleurone protoplasts to other species, we have determined the conditions necessary for the isolation of protoplasts from rice aleurone layers of germinated seed. Many of the common cell wall degrading enzymes used in making protoplasts were tested for their ability to release protoplasts from rice aleurone layers. Cellulysin was found to be the most effective. Transformation of these aleurone protoplasts was accomplished using polyethylene glycol and DNA constructs containing the firefly luciferase reporter gene under the control of two different promoters were tested. Luciferase expression was 24-fold greater when the reporter gene was under the control of the CaMV 35S promoter than when the promoter from the alcohol dehydrogenase 1 gene was used. With the isolation and transformation of aleurone protoplasts from rice, it is now possible to investigate molecular events occurring in this tissue during germination.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00234145
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  • 7
    Electronic Resource
    Electronic Resource
    Hairy roots of Brassica napus: I. Applied glutamine overcomes the effect of phosphinothricin treatment (1994)
    Springer
    Plant cell reports 14 (1994), S. 37-40 
    Details
    ISSN: 1432-203X
    Keywords: Ammonia ; Agrobacterium rhizogenes ; Brassica napus ; glutamine ; glutamine synthetase ; phosphinothricin ; rape
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Hairy roots of Brassica napus (rape cv. Giant) were produced by cocultivating leaf and cotyledon explants with Agrobacterium rhizogenes strain A4T. The hairy roots grew prolifically on solid and in liquid media. Incorporation of ammonium sulphate or phosphinothricin (PPT) into the media reduced growth. PPT treatment reduced glutamine synthetase (GS) activity and increased the ammonia content of the hairy roots. We have found that PPT treatment also induces a loss of glutamine from the roots and this may influence root growth. To test this we grew hairy roots in a liquid medium containing 10 mM glutamine. This glutamine treatment overcame the PPT induced suppression of growth but also significantly increased GS activity, reduced ammonia accumulation and increased the levels of glutamate and asparagine.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00233295
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  • 8
    Electronic Resource
    Electronic Resource
    Molecular improvement of cereals (1994)
    Springer
    Plant molecular biology 25 (1994), S. 925-937 
    Details
    ISSN: 1573-5028
    Keywords: cereals ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00014667
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  • 9
    Electronic Resource
    Electronic Resource
    The highly expressed tapetum-specific A9 gene is not required for male fertility in Brassica napus (1994)
    Springer
    Plant molecular biology 24 (1994), S. 97-104 
    Details
    ISSN: 1573-5028
    Keywords: anther ; antisense RNA ; Brassica napus ; male fertility ; tapetum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract An antisense approach was used to attempt to determine the function of the highly abundant, tapetum-specific A9 transcript in microsporogenesis. A Brassica napus A9 cDNA clone was linked in sense and antisense orientations to the Arabidopsis thaliana A9 promoter and the resulting chimaeric genes introduced into B. napus. A high proportion of the offspring of B. napus antisense A9 plants had very low or undetectable levels of A9 mRNA. However, these plants set seed and had pollen of normal or near normal viability. Therefore, under the conditions studied, the A9 protein appears not to be essential for male fertility in B. napus.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00040577
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  • 10
    Electronic Resource
    Electronic Resource
    Characterization of a mRNA that accumulates during development of oilseed rape pods (1994)
    Springer
    Plant molecular biology 24 (1994), S. 223-227 
    Details
    ISSN: 1573-5028
    Keywords: Brassica napus ; dehiscence ; dehydrogenase ; pod ; protochlorophyllide reductase ; shatter
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Dehiscence of oilseed rape pods, commonly known as pod shatter, is a process of agronomic importance that results in seed loss causing yield reductions and carry-over of the crop into the following growing season. In an effort to understand the mechanisms underlying this developmental event, the changes in gene expression that accompany pod shatter have been examined with a view to understanding how the process is regulated. In order to achieve this, a cDNA library was constructed using mRNA extracted from the dehiscence zone of developing pods. Differential screening with non-dehiscence zone cDNA led to the isolation of a pod-specific clone, SAC25, with a transcript size of 1100 nucleotide encoding a predicted polypeptide of 34 kDa. The level of SAC25 mRNA accumulation increased during pod development. The sequence shows no significant homology to others within the databases but has two identifiable amino acid motifs, one is an adenine nucleotide binding site for NAD/FAD dehydrogenases and the other is a conserved feature of the ribitol dehydrogenase family. The amino acid sequence has four putative glycosylation sites and contains four cysteine residues. Genomic Southern analysis indicates that SAC25 may be encoded by a single gene or a small gene family. The function of this mRNA is unknown but possible roles in dehiscence and pod development are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00040589
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  • 11
    Electronic Resource
    Electronic Resource
    Identification of conserved domains in the Δ12 desaturases of cyanobacteria (1994)
    Springer
    Plant molecular biology 24 (1994), S. 643-650 
    Details
    ISSN: 1573-5028
    Keywords: Anabaena variabilis ; fatty-acid desaturation ; Synechococcus PCC7002 ; Synechococcus PCC7942 ; Synechocystis PCC6714 ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Cyanobacterial genes for enzymes that desaturate fatty acids at the Δ12 position, designated desA, were isolated from Synechocystis PCC6714, Synechococcus PCC7002 and Anabaena variabilis by crosshybridization with a DNA probe derived from the desA gene of Synechocystis PCC6803. The genes of Synechocystis PCC6714, Synechococcus PCC7002 and A. variabilis encode proteins of 349, 347 and 350 amino acid residues, respectively. The transformation of Synechococcus PCC7942 with the desA genes from Synechocystis PCC6714, Synechococcus PCC7002 and A. variabilis was associated with the ability to introduce a second double bond at the Δ12 position of fatty acids. The amino acid sequence of the products of the desA genes revealed the presence of four conserved domains. Since one of the conserved domains was also found in the amino acid sequences of ω3 desaturases of Brassica napus and mung bean, this domain may play an essential role in the introduction of a double bond into fatty acids bound to membrane lipids.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00023560
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  • 12
    Electronic Resource
    Electronic Resource
    Directed disruption of the Chlamydomonas chloroplast psbK gene destabilizes the photosystem II reaction center complex (1994)
    Springer
    Plant molecular biology 24 (1994), S. 779-788 
    Details
    ISSN: 1573-5028
    Keywords: Chlamydomonas reinhardtii ; chloroplast ; transformation ; photosystem II ; psbK
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Using particle gun-mediated chloroplast transformation we have disrupted the psbK gene of Chlamydomonas reihardtii with an aadA expression cassette that confers resistance to spectinomycin. The transformants are unable to grow photoautotrophically, but they grow normally in acetate-containing medium. They are deficient in photosystem II activity as measured by fluorescence transients and O2 evolution and they accumulate less than 10% of wild-type levels of photosystem II as measured by immunochemical means. Pulse-labeling experiments indicate that the photosystem II complex is synthesized normally in the transformants. These results differ from those obtained previously with similar cyanobacterial psbK mutants that were still capable of photoautotrophic growth (Ikeuchi et al., J. Biol. Chem. 266 (1991) 1111–1115). In C. reinhardtii the psbK product is required for the stable assembly and/or stability of the photosystem II complex and essential for photoautotrophic growth. The data also suggest that the stability requirements of the photosynthetic complexes differ considerably between C. reinhardtii and cyanobacteria.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00029859
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  • 13
    Electronic Resource
    Electronic Resource
    A seed-specific Brassica napus oleosin promoter interacts with a G-box-specific protein and may be bi-directional (1994)
    Springer
    Plant molecular biology 24 (1994), S. 327-340 
    Details
    ISSN: 1573-5028
    Keywords: abscisic acid ; ABA-response element ; bi-directional promoter ; Brassica napus ; oleosin ; seed development
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In Brassica napus, oleosins are expressed at high levels in the seed during the latter stages of embryo development. The cis-acting regulatory properties of an 872 bp promoter fragment of a B. napus oleosin gene were examined by analysis of β-glucuronidase (GUS) expression in transgenic tobacco plants containing an oleosin promoter-GUS transcriptional fusion. The reporter gene was expressed at high levels only in seeds, specifically in embryo and endosperm tissue and regulated throughout seed development. These data demonstrate that oleosin gene transcription is regulated in a tissue-specific and temporally regulated manner and clearly indicate that oleosin protein expression is co-ordinated primarily at the transcriptional level. Oleosin mRNA was shown to be abscisic acid (ABA) inducible and an ABA-response element in the oleosin promoter was shown to be bound by a protein factor in a sequence-specific manner. Sequence analysis of the oleosin promoter has identified several other putative cis-acting sequences which may direct oleosin gene expression. The presence of a large open reading frame in the bottom strand of the oleosin promoter (ORF2) which encodes a polypeptide similar to the ethylene-induced E4 gene of tomato is reported. A PCR-generated DNA probe containing the ORF2 sequence hybridised with a 1.4 kb transcript in total RNA extracts of a variety of tissues, including leaves and germinated seed cotyledons. This finding suggests that the oleosin gene promoter directs transcription in both directions. It is the first report of a bi-directional nuclear gene promoter in plants.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00020171
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  • 14
    Electronic Resource
    Electronic Resource
    Stable transformation and long-term expression of the gusA reporter gene in callus lines of perennial ryegrass (Lolium perenne L.) (1994)
    Springer
    Plant molecular biology 24 (1994), S. 401-405 
    Details
    ISSN: 1573-5028
    Keywords: Lolium perenne L. ; transformation ; rice gene GOS2 ; long-term GUS expression
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Stable transformation of perennial ryegrass (Lolium perenne L.) was achieved by biolistic bombardment of a non embryogenic cell suspension culture, using the hpt and gusA gene. The transformation yielded on the average 5 callus lines per bombardment (1.4×106 cells). Stable integration of the genes into the plant genome was demonstrated by Southern analysis of DNA, isolated from hygromycin-resistant callus lines. The gusA reporter gene, which was regulated by the constitutive promoter of the rice gene GOS2, was expressed in both transient and stable transformation assays, indicating that this promoter is suitable for expression of a transferred gene in perennial ryegrass. Long-term GUS expression was observed in ca. 40% of the callus lines, whereas the other callus lines showed instability after 6 months and 1 year of culture.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00020178
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  • 15
    Electronic Resource
    Electronic Resource
    Structure and function of selectable and non-selectable transgenes in maize after introduction by particle bombardment (1994)
    Springer
    Plant molecular biology 25 (1994), S. 951-961 
    Details
    ISSN: 1573-5028
    Keywords: Cell biology ; epigenetics ; maize ; transformation ; transgenes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Zea mays transformants produced by particle bombardment of embryogenic suspension culture cells of the genotype A188 × B73 and selected on kanamycin or bialaphos were characterized with respect to transgene integration, expression, and inheritance. Selection on bialaphos, mediated by thebar orpat genes, was more efficient than selection on kanamycin, mediated by thenptII gene. Most transformants contained multicopy, single locus, transgene insertion events. A transgene expression cassette was more likely to be rearranged if expression of that gene was not selected for during callus growth. Not all plants regenerated from calli representing single transformation events expressed the transgenes, and a non-selectable gene (uidA) was expressed in fewer plants than was the selectable transgene. Mendelian inheritance of transgenes consistent with transgene insertion at a single locus was observed for approximately two thirds of the transformants assessed. Transgene expression was typically, but not always, predictable in progeny plants-transgene silencing, as well as poor transgene transmission to progeny, was observed in some plant lines in which the parent plants had expressed the transgene.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00014669
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  • 16
    Electronic Resource
    Electronic Resource
    Expression of mRNA and steady-state levels of protein isoforms of enoyl-ACP reductase from Brassica napus (1994)
    Springer
    Plant molecular biology 26 (1994), S. 155-163 
    Details
    ISSN: 1573-5028
    Keywords: Brassica napus ; Enoyl-ACP reductase ; isoforms ; stearoyl-ACP desaturase ; developmental expression ; seed
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The expression of mRNA and the steady-state levels of two-component enzymes of plant fatty acid synthetase (FAS) were studied. Northern analysis of enoyl-ACP reductase (ER) and stearoyl-ACP desaturase (SD) gene expression showed that steady-state levels of both transcripts increase during lipid deposition in the seed reaching a maximum at 29 days after flowering (DAF). The steady-state level of ER message falls very quickly after reaching its maximum, whereas the SD message is longer-lived. The levels of these specific mRNAs in seed are 15–30 times greater than in leaf. Optimum mRNA expression precedes the maximum levels of synthesis of the two proteins, which in turn precede the maximum level of oil. The expression of isoenzymes of ER were examined by two-dimensional western blotting in both leaf and seed tissue. Four enzymes are expressed in both of these tissues; the two most abundant isoforms in seed material are also the most abundant in leaf tissue.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00039528
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  • 17
    Electronic Resource
    Electronic Resource
    Cloning of ω3 desaturase from cyanobacteria and its use in altering the degree of membrane-lipid unsaturation (1994)
    Springer
    Plant molecular biology 26 (1994), S. 249-263 
    Details
    ISSN: 1573-5028
    Keywords: desB gene ; desaturase ; fatty acid ; Synechococcus sp. PCC 7942 ; Synechocystis sp. PCC 6803 ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Cyanobacteria respond to a decrease in temperature by desaturating fatty acids of membrane lipids to compensate for the decrease in membrane fluidity. Among various desaturation reactions in cyanobacteria, the desaturation of the ω3 position of fatty acids is the most sensitive to the change in temperature. In the present study, we isolated a gene, designated desB, for the ω3 desaturase from the cyanobacterium, Synechocystis sp. PCC 6803. The desB gene encodes a protein a 359 amino-acid residues with molecular mass of 41.9 kDa. The desB gene is transcribed as a monocistronic operon that produced a single transcript of 1.4 kb. The level of the desB transcript in cells grown at 22°C was 10 times higher than that in cells grown at 34°C. In order to manipulate the fatty-acid unsaturation of membrane lipids, the desB gene in Synechocystis sp. PCC 6803 was mutated by insertion of a kanamycin-resistance gene cartridge. The resultant mutant was unable to desaturate fatty acids at the ω3 position. The desA gene, which encodes the Δ12 desaturase of Synechocystis sp. PCC 6803, and the desB gene were introduced into Synechococcus sp. PCC 7942. Whilst the parent cyanobacterium can only desaturate membrane lipids at the Δ9 position of fatty acids, the resultant transformant was able to desaturate fatty acids of membrane lipids at the Δ9, Δ12 and ω3 positions. These results confirm the function of the desB gene and demonstrate that it is possible to genetically manipulate the fatty-acid unsaturation of membrane lipids in cyanobacteria.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00039536
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  • 18
    Electronic Resource
    Electronic Resource
    Effects of an antisense napin gene on seed storage compounds in transgenic Brassica napus seeds (1994)
    Springer
    Plant molecular biology 26 (1994), S. 1115-1124 
    Details
    ISSN: 1573-5028
    Keywords: Brassica napus ; napin ; antisense ; seed storage protein ; seed storage lipid
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract To manipulate the quantity and quality of storage components in Brassica napus seeds, we have constructed an antisense gene for the storage protein napin. The antisense gene was driven by the 5′-flanking region of the B. napus napin gene to express antisense RNA in a seed-specific manner. Seeds of transgenic plants with antisense genes often contained reduced amounts of napin. In some transgenic plants, no accumulation of napin was observed. However, the total protein content of transgenic and wild-type seeds did not differ significantly. Seeds lacking napin accumulated 1.4 to 1.5 times more cruciferin than untransformed seeds, although the oleosin content was not affected. Fatty acid content and composition in the seeds of transgenic plants were also analyzed by gas chromatography. Though the total fatty acid content of the transformants was the same as that of non-transformants, there was a reduction in 18:1 contents and a concomitant increase of 18:2 in seeds with reduced napin levels. This observed change in fatty acid composition was inherited in the next generation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00040693
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  • 19
    Electronic Resource
    Electronic Resource
    Functional complementation of a yeast vesicular transport mutation ypt1-1 by a Brassica napus cDNA clone encoding a small GTP-binding protein (1994)
    Springer
    Plant molecular biology 26 (1994), S. 1725-1735 
    Details
    ISSN: 1573-5028
    Keywords: Brassica napus ; heterologous expression ; Rab/Ypt family ; small GTP-binding protein ; vesicular transport
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A cDNA clone (bra) encoding a small GTP-binding protein was isolated from Brassica napus by screening a root cDNA library with a degenerate oligonucleotide probe that corresponds to a highly conserved GTP-binding domain of the Ras superfamily. Sequence analysis shows that the clone contains an open reading frame of 219 amino acid residues with the estimated molecular mass of 24379 Da and this coding region contains all the conserved motifs of the Ras superfamily. The deduced amino acid sequence of the bra gene is most closely related to the Ypt/Rab family that functions in the vesicular transport (46% and 47% amino acid identity to the yeast Ypt1 and to the human Rab1, respectively) and is more distantly related to the other Ras-related families. The protein encoded by the bra gene, when expressed in Escherichia coli, shows the ability to bind GTP. Furthermore, when the bra gene is introduced into Saccharomyces cerevisiae under the regulation of the yeast GAL1 promoter, the gene can complement the temperature-sensitive yeast mutation ypt1-1 that has defects in vesicular transport function. The amino acid sequence similarity and the functional complementation of the yeast mutation suggest that this gene is likely to be involved in the vesicular transport in plants. Genomic Southern analysis shows that this gene is a member of a small gene family in Brassica napus.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00019487
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  • 20
    Electronic Resource
    Electronic Resource
    Cotton (Gossypium hirsutum L.) pollen-specific polygalacturonase mRNA: tissue and temporal specificity of its promoter in transgenic tobacco (1994)
    Springer
    Plant molecular biology 26 (1994), S. 1989-1993 
    Details
    ISSN: 1573-5028
    Keywords: polygalacturonase ; pollen-specific promoter ; cotton ; transgenics ; transformation ; β-glucuronidase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A gene (G9) expressed during late microsporogenesis in cotton (Gossypium hirsutum L.) was isolated. Sequence analysis of the cDNA (1.3 kb) as well as the gene (2.6 kb) revealed an open reading frame of 1233 bases encoding a protein of 43.9 kDa. The coding region of the gene is interrupted by three introns. Northern analysis of the RNA from developing anthers showed that the transcripts appear 12 days before anthesis and that the maximal concentration of RNA occurs in pollen on the day of anthesis. This pattern of gene expression suggests functions in post-anthesis events. Sequence comparisons with other known plant genes indicated that G9 is homologous to polygalacturonases. The G9 promoter conferred tissue and temporal specificity of β-glucuronidase (GUS) expression in transgenic tobacco plants. Thus, the G9 promoter can be used to drive gene expression in homologous as well as heterologous plants in a tissue-specific manner.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00019509
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  • 21
    Electronic Resource
    Electronic Resource
    Expression of the tobacco Tnt1 retrotransposon promoter in heterologous species (1994)
    Springer
    Plant molecular biology 26 (1994), S. 393-402 
    Details
    ISSN: 1573-5028
    Keywords: Arabidopsis thaliana ; Brassica napus ; gene expression ; Nicotiana tabacum ; retrotransposon
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The expression of the tobacco (Nicotiana tabacum) retrotransposon Tntl has previously been shown to be strongly regulated and driven from the 5′ long terminal repeat (LTR). We report here that the Tntl LTR can promote activity of the β-glucuronidase (GUS) reporter gene in two heterologous species of the Brassicaceae family, namely rapessed (Brassica napus) and Arabidopsis thaliana. The translational LTR-GUS fusion was active in transient expression studies performed with tobacco and rapeseed protoplasts, indicating that the LTR sequences are recognized in heterologous species. Our results also showed that Tntl LTR-promoted GUS expression in transgenic Arabidopsis is strongly regulated, and that, in contrast to tobacco, hormonal activation plays a significant role in the expression of the Tntl LTR in Arabidopsis. LTR sequences were shown to be more effective than the CaMV 35S enhancer region in transient expression studies performed with tobacco or rapessed protoplasts; and substitution of the LTR sequences upstream from the major transcriptional start with the CaMV 35S enhancer region gave high levels of expression in transgenic tobacco and Arabidopsis leaves, suggesting that a Tntl element with similar substitutions in its 5′ LTR might be suited for gene-tagging experiments in heterologous species.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00039548
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  • 22
    Electronic Resource
    Electronic Resource
    Molecular analysis of two Brassica napus genes expressed in the stigma (1994)
    Springer
    Plant molecular biology 26 (1994), S. 1217-1222 
    Details
    ISSN: 1573-5028
    Keywords: Brassica napus ; pistil ; stigma ; cDNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A partial cDNA clone, Pis 63, corresponding to a mRNA highly expressed in Brassica napus pistils, was isolated by differential screening. PCR was used to complete the Pis 63 sequence (Pis 63-1) and to obtain the sequence of another related cDNA (Pis 63-2). Northern blot and in situ analyses demonstrated that these transcripts are expressed in the stigma throughout flower development. Pis 63-1 and Pis 63-2 display similarity to a cotton fibre cDNA clone.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00040703
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  • 23
    Electronic Resource
    Electronic Resource
    Expression of the BnmNAP subfamily of napin genes coincides with the induction of Brassica microspore embryogenesis (1994)
    Springer
    Plant molecular biology 26 (1994), S. 1711-1723 
    Details
    ISSN: 1573-5028
    Keywords: Brassica napus ; microspore embryogenesis ; napin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Brassica napus cv. Topas microspores can be diverted from pollen development toward haploid embryo formation in culture by subjecting them to a heat stress treatment. We show that this switch in developmental pathways is accompanied by the induction of high levels of napin seed storage protein gene expression. Changes in the plant growth or microspore culture conditions were not by themselves sufficient to induce napin gene expression. Specific members of the napin multigene family were cloned from a cDNA library prepared from microspores that had been induced to undergo embryogenesis. The majority of napin clones represented three members (BnmNAP2, BnmNAP3 and BnmNAP4) that, along with a previously isolated napin genomic clone (BngNAP1), constitute the highly conserved BnmNAP subfamily of napin genes. Both RNA gel blot analysis, using a subfamily-specific probe, and histochemical analysis of transgenic plants expressing a BngNAP1 promoter-β-glucuronidase gene fusion demonstrated that the BnmNAP subfamily is expressed in embryogenic microspores as well as during subsequent stages of microsporic embryo development.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00019486
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  • 24
    Electronic Resource
    Electronic Resource
    Production of fertile transgenic maize by electroporation of suspension culture cells (1994)
    Springer
    Plant molecular biology 24 (1994), S. 51-61 
    Details
    ISSN: 1573-5028
    Keywords: Zea mays L. ; transformation ; electroporation ; bar ; phosphinothricin acetyltransferase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Fertile, transgenic maize plants were generated by electroporation of suspension culture cells that were treated with a pectin-degrading enzyme. Electroporation of cells from two different suspension cultures, one derived from A188 X B73 and one derived from a B73-related inbred, with a plasmid containing the bar gene, resulted in high-frequency recovery of stably transformed callus lines. Plants were regenerated from thirteen transformed callus lines and transmission of bar to progeny was demonstrated.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00040573
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  • 25
    Electronic Resource
    Electronic Resource
    Molecular cloning of a cDNA fromBrassica napus L. for a homologue of acyl-CoA-binding protein (1994)
    Springer
    Plant molecular biology 25 (1994), S. 917-920 
    Details
    ISSN: 1573-5028
    Keywords: acyl-CoA-binding protein ; Brassica napus ; diazepam-binding inhibitor protein ; linkage map
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A cDNA encoding an acyl-CoA-binding protein (ACBP) homologue has been cloned from a λgt11 library made from mRNA isolated from developing seeds of oilseed rape (Brassica napus L.). The derived amino acid sequence reveals a protein 92 amino acids in length which is highly conserved when compared with ACBP sequences from yeast, cow, man and fruit fly. Southern blot analysis ofBrassica napus genomic DNA revealed the presence of 6 genes, 3 derived from theBrassica rapa parent and 3 fromBrassica oleracea. Northern blot analysis showed that ACBP genes are expressed strongly in developing embryo, flowers and cotyledons of seedlings and to a lesser extent in leaves and roots.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00028886
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  • 26
    Electronic Resource
    Electronic Resource
    Hairy roots of Brassica napus: II. Glutamine synthetase overexpression alters ammonia assimilation and the response to phosphinothricin (1994)
    Springer
    Plant cell reports 14 (1994), S. 41-46 
    Details
    ISSN: 1432-203X
    Keywords: Agrobacterium rhizogenes ; Brassica napus ; glutamine synthetase ; phosphinothricin ; rape ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Hairy roots of Brassica napus (rape cv. Giant) have been produced that contain the cytosolic glutamine synthetase (GS) gene from Glycine max (soybean). Leaf explants were cocultivated with Agrobacterium rhizogenes strain A4T harbouring the binary vector pLN16. This vector was constructed by inserting a soybean cytosolic GS cDNA into the multiple cloning site of pGA643, placing it under the control of the CaMV promoter. In addition, the T-DNA region of pLN16 contained a NPTII gene for selection of transformed cells. Transgenic hairy roots grew prolifically on hormone-free media containing a selective level of kanamycin. Southern and northern analyses confirmed the presence of soybean GS DNA and transcripts, respectively. These transformed hairy roots also have a greater abundance of the GS polypeptide, approximately 3–6 fold greater GS activity and lower levels of endogenous ammonia. Hairy roots provide a useful system for studying responses to phosphinothricin (PPT). Hairy roots grown in media containing PPT had lower GS activity, greater ammonia accumulation and slower growth than controls. The presence of the soybean GS gene in the hairy roots reduced these PPT-induced effects and resulted in higher GS activity, lower ammonia levels and faster growth than in PPT-treated controls. Greater tolerance of PPT was also seen in shoots regenerated from the hairy roots displaying elevated levels of GS activity.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00233296
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  • 27
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    Electronic Resource
    Discrimination among cultivars of rapeseed (Brassica napus L.) using DNA polymorphisms amplified from arbitrary primers (1994)
    Springer
    Theoretical and applied genetics 87 (1994), S. 697-704 
    Details
    ISSN: 1432-2242
    Keywords: Brassica napus ; Cultivar identification ; RAPDs ; Rapeseed ; Taxonomy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract RAPDs (Randomly Amplified Polymorphic DNAs) were used to discriminate among 23 cultivars of oilseed rape (Brassica napus) selected from several breeding programs. A set of 100 random sequence 10-mer primers were tested, of which 70 produced bands and 22 showed evidence of polymorphism. A selection of six primers produced 23 polymorphic bands of between 300 to 2200 base pairs in size, sufficient to distinguish between the cultivars. An analysis of seed of five cultivars obtained from four different sites showed stability of banding pattern over source of seed. The analysis was repeated using four different thermocyclers, each of which produced the same band pattern. UPGMA cluster analysis indicates that the relationships among some of the cultivars is closer for those from the same breeding program than for those from different programs. The results of this study show that RAPDs can be used as a method of identification for oilseed rape cultivars.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00222895
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  • 28
    Electronic Resource
    Electronic Resource
    Evaluation of RFLP and RAPD markers in a comparison of Brassica napus breeding lines (1994)
    Springer
    Theoretical and applied genetics 88 (1994), S. 123-128 
    Details
    ISSN: 1432-2242
    Keywords: Brassica napus ; RFLP markers ; RAPD markers ; Genetic distance
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract RFLP and RAPD markers were evaluated and compared for their ability to determine genetic relationships in a set of three B. napus breeding lines. Using a total of 50 RFLP and 92 RAPD markers, the relatedness between the lines was determined. In total, the RFLP and the RAPD analysis revealed more than 500 and 400 bands, respectively. The relative frequencies of loci with allele differences were estimated from the band data. The RFLP and RAPD marker sets detected very similar relationships among the three lines, consistent with known pedigree data. Bootstrap analyses showed that the use of approximately 30 probes or primers would have been sufficient to achieve these relationships. This indicates that RAPD markers have the same resolving power as RFLP markers when used on exactly the same set of B. napus genotypes. Since RAPD markers are easier and quicker to use, these markers may be preferred in applications where the relationships between closely-related breeding lines are of interest. The use of RAPD markers in fingerprinting applications may, however, not be warranted, and this is discussed in relation to the reliability of RAPD markers.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00222404
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  • 29
    Electronic Resource
    Electronic Resource
    Genetic diversity of oilseedBrassica napus germ plasm based on restriction fragment length polymorphisms (1994)
    Springer
    Theoretical and applied genetics 88 (1994), S. 662-668 
    Details
    ISSN: 1432-2242
    Keywords: Oilseed rape ; Brassica napus ; Restriction fragment length polymorphism ; Genetic diversity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Oilseed rape (Brassica napus) is an important oilseed crop worldwide. Cultivars have been developed for many growing regions, however little is known about genetic diversity inB. napus germ plasm. The purpose of the research presented here was to study the genetic diversity and relationships ofB. napus accessions using restriction fragment length polymorphisms (RFLPs). Eighty threeB. napus accessions were screened using 43 genomic DNA clones which revealed 161 polymorphic fragments. Each accession was uniquely identified by the markers with the exception of the near-isogenic cvs ‘Triton’ and ‘Tower’. The RFLP data were analyzed by cluster analysis of similarity coefficients and by principal component analysis. Overall, there were three major groups of cultivars. The first group included only spring accessions, the second mostly winter accessions and the third, rutabagas and oilseed rape accessions from China and Japan. These results indicate that withinB. napus, winter and spring cultivars represent genetically distinct groups. The grouping of accessions by cluster analysis was generally consistent with known pedigrees. This consistency included the grouping of lines derived both by backcrossing or self-pollination with their parents.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01253968
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  • 30
    Electronic Resource
    Electronic Resource
    Identification of RAPD markers linked to a fertility restorer gene for theOgura radish cytoplasmic male sterility of rapeseed (Brassica napus L.) (1994)
    Springer
    Theoretical and applied genetics 88 (1994), S. 741-748 
    Details
    ISSN: 1432-2242
    Keywords: Brassica napus ; Raphanus sativus ; Ogura cytoplasmic male-sterility restorer gene ; Bulked segregant analysis ; RAPD markers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Bulked segregant analysis was employed to identify random amplified polymorphic DNA (RAPD) markers linked to the restorer gene (Rfo) used in theOgura radish cytoplasmic male sterility of rapeseed. A total of 138 arbitrary 10-mer oligonucleotide primers were screened on the DNA of three pairs of bulks, each bulk corresponding to homozygous restored and male sterile plants of three segregating populations. Six primers produced repeatable polymorphisms between paired bulks. DNA from individual plants of each bulk was then used as a template for amplification with these six primers. DNA polymorphisms generated by four of these primers were found to be completely linked to the restorer gene with the polymorphic DNA fragments being associated either with the fertility restorer allele or with the sterility maintainer allele. Pairwise cross-hybridization demonstrated that the four polymorphic DNA fragments did not share any homology. Southern hybridization of labelled RAPD fragments on digested genomic DNA from the same three pairs of bulks revealed fragments specific to either the male sterile bulks or to the restored bulks and a few fragments common to all bulks, indicating that the amplified sequences are low copy. The four RAPD fragments that were completely linked to the restorer locus have been cloned and sequenced to develop sequence characterized amplified regions (SCARs). This will facilitate the construction of restorer lines used in breeding programs and is the first step towards map-based cloning of the fertility restorer allele.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01253979
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  • 31
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    Electronic Resource
    A simple method to estimate the percentage of hybridity in canola (Brassica napus) F1 hybrids (1994)
    Springer
    Theoretical and applied genetics 89 (1994), S. 853-858 
    Details
    ISSN: 1432-2242
    Keywords: Polymerase chain reaction ; Random amplified polymorphic DNA ; Self-incompatibility ; Brassica campestris ; Brassica napus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have developed an efficient PCR-based system that uses RAPD markers for the certification of F1 hybrids of canola. These markers were selected by screening five parental lines used in three crosses X, Y and Z with 131, 131 and 322 primers respectively. Stable DNA fragments that were homozygous and specific to the male inbreds were used to certify F1 hybrid populations. The hybrid production system was based on self-incompatibility (SI) alleles that prevent self-pollination of the female parent. The efficiency of two S-alleles was compared under both field and greenhouse conditions. The percentage of hybridity was estimated in different F1 populations. We found a significant difference between the two alleles for their efficiency in controlling selfing; both alleles were stable under greenhouse conditions, one allele appeared less reliable under field conditions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00224508
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  • 32
    Electronic Resource
    Electronic Resource
    RFLP mapping of Brassica napus using doubled haploid lines (1994)
    Springer
    Theoretical and applied genetics 89 (1994), S. 615-621 
    Details
    ISSN: 1432-2242
    Keywords: Brassica napus ; Doubled haploid ; Linkage map ; Restriction fragment length polymorphism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The combined use of doubled haploid lines and molecular markers can provide new genetic information for use in breeding programs. An F1-derived doubled haploid (DH) population of Brassica napus obtained from a cross between an annual canola cultivar (‘Stellar’) and a biennial rapeseed (‘Major’) was used to construct a linkage map of 132 restriction fragment length polymorphism loci. The marker loci were arranged into 22 linkage groups and six pairs of linked loci covering 1016 cM. The DH map was compared to a partial map constructed with a common set of markers for an F2 population derived from the same F1 plant, and the overall maps were not significantly different. Comparisons of maps in Brassica species suggest that less recombination occurs in B. napus (n = 19) than expected from the combined map distances of the two hypothesized diploid progenitors, B. oleracea (n = 9) and B. rapa (n=10). A high percentage (32%) of segregating marker loci were duplicated in the DH map, and conserved linkage arrangements of some duplicated loci indicated possible intergenome homoeology in the amphidiploid or intragenome duplications from the diploid progenitors. Deviation from Mendelian segregation ratios (P 〈 0.05) was observed for 30% of the marker loci in the DH population and for 24% in the F2 population. Deviation towards each parent occurred at equal frequencies in both populations and marker loci that showed deviation clustered in specific linkage groups. The DH lines and molecular marker map generated for this study can be used to map loci for agronomic traits segregating in this population.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00222456
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  • 33
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    Electronic Resource
    Inbreeding depression and dominance-suppression competition after inbreeding in rapeseed (Brassica napus) (1994)
    Springer
    Theoretical and applied genetics 88 (1994), S. 321-323 
    Details
    ISSN: 1432-2242
    Keywords: Brassica napus ; Inbreeding ; Inbreeding depression ; Line variation ; Competition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Rapeseed plants, of the summer annual variety Topas, that had been selfed twice consecutively were compared to outcrossed half-sibs for inbreeding depression in a rapeseed population at mating equilibrium. The effect of dominance-suppression competition was included in the effect of inbreeding. Both female-and male-fitness characters showed significant inbreeding depression. Biomass decreased 17% with inbreeding and was highly correlated with seed weight. The total number of flowers decreased 15% with inbreeding. There was a significant effect of lines. The possible importance of experimental design in studies that estimate inbreeding depression is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00223639
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  • 34
    Electronic Resource
    Electronic Resource
    Intergeneric hybridization between Brassica napus and Sinapis pubescens, and the cytology and crossability of their progenies (1994)
    Springer
    Theoretical and applied genetics 89 (1994), S. 540-544 
    Details
    ISSN: 1432-2242
    Keywords: Brassica napus ; Crossability ; Cytogenetics ; Intergeneric hybridization ; Sinapis pubescens
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The cytological possibility of gene transfer from Sinapis pubescens to Brassica napus was investigated. Intergeneric hybrids between Brassica napus (2n = 38) and Sinapis pubescens (2n = 18) were produced through ovary culture. The F1 hybrids were dihaploid and the chromosome configurations were (0–1) III + (2–11) II + (5–24) I . One F2 plant with 38 chromosomes was obtained from open pollination of the F1 hybrid. Thirty-one seeds were obtained from the backcross of the F2 plant with B. napus. Five out of seven plants had 38 chromosomes, and the pollen stainability ranged from 0% to 81.4%. In the B2 plants obtained from the backcross of B1 plants with B. napus, 66.7% of the plants examined had 38 chromosomes. S. pubescens may become a gene source for the improvement of B. napus.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00222445
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  • 35
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    Electronic Resource
    T-DNA-insert-independent mutations induced in transformed plant cells duringAgrobacterium co-cultivation (1994)
    Springer
    Transgenic research 3 (1994), S. 317-325 
    Details
    ISSN: 1573-9368
    Keywords: Agrobacterium ; mutagenesis ; Nicotiana plumbaginifolia ; nitrate reductase ; ploidy ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Transformation frequencies were determined for 1n, 2n, and 4n Nicotiana plumbaginifolia protoplast cultures inAgrobacterium-mediated gene transfer experiments. An unexpected large drop (50%) in plating efficiencies was observed in the non-selected (control) 1n populations after transformation treatment with virulent strains. This effect was not observed in the 2n or 4n cultures or in the 1n cultures when treated with avirulent bacteria. The mortality was disproportionally high and could not be explained by the low (0.1–0.5%) transformation efficiency in the 1n population, indicating mutagenesis of the cell populations independently from the T-DNA insertions. Mutagenesis was also indicated in gene tagging experiments where nitrate reductase-deficient (NR−) mutants were selected from haploidNicotiana plumbaginifolia protoplasts, as well as from leaf disc cultures or protoplasts of diploid plants that were heterozygotic for a mutation either in the NR apoenzyme gene (nia/wt) or one of the molybdenum-containing cofactor genes (cnxA/wt), afterAgrobacterium co-cultivation. The chlorate-resistant isolates were tested for the T-DNA-specific kanamycin resistance trait only after NR-deficiency had been established. Thirty-nine independent NR-deficient mutants were analysed further by Southern blot hybridization. There was no indication of integrated T-DNA sequences in the mutated NR genes, despite the fact that NR-deficient cells were found more frequently in cell populations which became transformed during the treatment than in the populations which did not. These observations suggest that transformation-competent cells undergo mutagenesis during theAgrobacterium gene transfer process not only as a result of stable integration events, but also through accompanying events that do not result in major changes in the mutated loci. The nature of these changes at the molecular level remains to be elucidated.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01973592
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    Electronic Resource
    An assessment of gene transfer by pollen from field-grown transgenic potatoes to non-transgenic potatoes and related species (1994)
    Springer
    Transgenic research 3 (1994), S. 216-225 
    Details
    ISSN: 1573-9368
    Keywords: Solanum tuberosum ; genetic modification ; transformation ; gene transfer ; genetic isolation ; risk assessment
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Information on the extent of transgene dispersal by pollen to adjacent potato plots and to related weed species is an important requisite for risk assessment; a procedure followed before novel transgenic plants are evaluated under field conditions. The purpose of the investigation was to determine the frequency of cross-pollination between potato (Solanum tuberosum) plants at different distances, using a kanamycin resistnace transgene (nptII) as a selectable marker. All potato plants were from the variety Désirée. Non-transgenic potato plants, used as potential recipients of transgene-containing pollen, were planted in 12 sub-plots, at distances of 0–20 m from the nearest transgenic potato plants. Seeds harvested from the non-transgenic plants were screened for resistance to kanamycin, and molecular methods were used to confirm that resistant progeny contained thenptII gene. Where transgenic and non-transgenic potato plants were in alternate rows (leaves touching), 24% of seedlings from the non-transgenic parent plants were kanamycin-resistant. Comparable seedlings from plants at up to 3 m distance had a resistance frequency of 2%, at 10 m the frequency was 0.017% and at 20 m no resistant progeny were observed. Plants of the weed speciesS. dulcamara andS. nigrum were also planted close to the transgenic potatoes to test for evidence of hybridization, and no kanamycin-resistant seedlings were observed among progeny fromS. dulcamara andS. nigrum. This investigation provided evidence that the extent of gene dispersal from transgenic potatoes to non-transgenic potatoes falls markedly with increasing distance, and is negligible at 10 m. There was, also, no evidence of transgene movement from potato toS. dulcamara andS. nigrum under field conditions. These data will be valuable in defining genetic isolation procedures for the early field evaluation and the use of novel transgenic potato genotypes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02336774
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  • 37
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    Opportunities for gene transfer from transgenic oilseed rape (Brassica napus) to related species (1994)
    Springer
    Transgenic research 3 (1994), S. 263-278 
    Details
    ISSN: 1573-9368
    Keywords: Brassica napus ; oilseed rape ; transgenic plants ; interspecific hybridization ; gene transfer ; risk assessment
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Before novel transgenic plant genotypes are grown outside containment facilities and evaluated under field conditions, it is necessary to complete a risk assessment to consider the possible consequences of that release. An important aspect of risk assessment is to consider the likelihood and consequences of the transgene being transferred by cross-pollination to related species, including other crops, weeds and ruderal populations. The purpose of this report is to review the literature to assess the ease with whichBrassica napus can hybridize with related species. The evidence for hybridization is considered at three levels: a) by open pollination, b) by hand pollination and c) by the use ofin vitro ovule and embryo rescue techniques; and also examines the fertility and vigour of the F1, F2 and backcross generations. Four species are reported to hybridize withB. napus by open pollination:B. rapa andB. juncea using fully fertile parents; andB. adpressa andR. raphanistrum using a male-sterileB. napus parent. Seventeen species are reported to form hybrids (including the four species above) withB. napus when pollination is carried out manually. At least 12 of these species were unable to form F2 progeny, and eight were unable to produce progeny when the F1 was backcrossed to one of the parental species. Many factors will influence the success of hybridization under field conditions, including: distance between the parents, synchrony of flowering, method of pollen spread, specific parental genotypes used, direction of the cross and the environmental conditions. Even where there is a possibility of hybridization betweenB. napus and a related species growing in the vicinity of a release, poor vigour and high sterility in the hybrids will generally mean that hybrids and their progeny will not survive in either an agricultural or natural habitat.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01973586
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  • 38
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    Electronic Resource
    Actin microfilament organization during pollen development ofBrassica napus cv. Topas (1994)
    Springer
    Protoplasma 183 (1994), S. 67-76 
    Details
    ISSN: 1615-6102
    Keywords: Actin microfilaments ; Brassica napus ; Cytochalasin D ; Pollen development
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The organization of actin microfilaments (MFs) was studied during pollen development ofBrassica napus cv. Topas. Cells were prepared using three techniques and double labelled for fluorescence microscopy with rhodamine-labelled phalloidin for MFs and Hoechst 33258 for DNA. Microfilaments are present at all stages of pollen development with the exception of tricellular pollen just prior to anthesis. Unicellular microspores contain MFs which radiate from the surface of the nuclear envelope into the cytoplasm. During mitosis MFs form a network partially surrounding the mitotic apparatus and extend into the cytoplasm. Both cytoplasmic and phragmoplast-associated MFs are present during cytokinesis. Nuclear associated-, cytoplasmic, and randomly oriented cortical MFs appear in the vegetative cell of the bicellular microspore. Cortical MFs in the vegetative cell organize into parallel MF bundles (MFBs) aligned transverse to the furrows. The MFBs disappear prior to microspore elongation. At anthesis MFs are restricted to the cortical areas subjacent to the furrows of the vegetative cell. The use of cytochalasin D to disrupt MF function resulted in: (1) displacement of the acentric nucleus in the unicellular microspore; (2) displacement of the spindle apparatus in the mitotic cell; (3) symmetrical growth of the bicellular microspore rather than elongation and (4) inhibition of pollen tube germination in the mature pollen grain. This suggests that MFs play an important role in anchoring the nucleus in the unicellular microspore as well as the spindle apparatus during microspore mitosis, in microspore shape determination and in pollen tube germination.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01276814
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  • 39
    Electronic Resource
    Electronic Resource
    Recombinant viruses as transformation vectors of marine macroalgae (1994)
    Springer
    Journal of applied phycology 6 (1994), S. 247-253 
    Details
    ISSN: 1573-5176
    Keywords: algae ; genes ; recombinant ; transformation ; vectors ; viruses
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The large dsDNA viruses that are known to infect eukaryotic algae show promise as genetic vectors for algal biotechnology. The large size (150–330 kbp) of these viral genomes may permit insertion of large sequences of foreign DNA. The viruses infecting filamentous marine brown algae appear to be integrated into the genomes of their hosts, and may provide integration mechanisms that can be used for directing insertion of foreign genes into algal chromosomes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02186078
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  • 40
    Electronic Resource
    Electronic Resource
    Maintenance and expression of heterologous genes in chloroplast ofChlamydomonas reinhardtii (1994)
    Springer
    Journal of applied phycology 6 (1994), S. 239-245 
    Details
    ISSN: 1573-5176
    Keywords: Chlamydomonas reinhardtii ; transformation ; chloroplast ; aminoglycoside adenine transferase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The chloroplast genome ofChlamydomonas reinhardtii has been transformed with a chimeric gene consisting of the chloroplastatpA promoter and the bacterial gene for aminoglycoside adenine transferase (aadA). TheatpA-aadA cassette has been placed within the chloroplast DNAEcoRI restriction enzyme fragment 14, or within the chloroplastBamH1 fragment 10. The chimeric constructs were introduced into the chloroplast by particle bombardment. Integration of the cassette into chloroplast DNA then occurred via homologous recombination of sequences flanking the cassette with their corresponding chloroplast sequences. We demonstrate that the chloroplastatpA promoter inatpA-aadA routinely recombines with its endogenous counterpart, resulting in heteroplasmic chloroplast DNA populations that may persist for many generations. The heterologous gene does not require a 3′ inverted repeat sequence for its expression. TheatpA-aadA gene copy number, which is dictated here by its position in the chloroplast genome, is proportional to the steady state level ofatpA-aadA mRNA. However, neither genomic position, gene copy number, or mRNA level have a significant effect on cellular resistance to spectinomycin, nor activity of theaadA gene productin vitro. These results suggest that, in the case ofaadA, the limiting step for expression of this gene is at the translational or post-translational level. TheatpA-aadA cassette should prove a useful model for future studies on the maintenance and expression of heterologous genes inC. reinhardtii chloroplasts.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02186077
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  • 41
    Electronic Resource
    Electronic Resource
    A simple technique for producing 13C or 14C-labelled fronds of Lemna gibba and their use in soil incubation investigations (1994)
    Springer
    Plant and soil 160 (1994), S. 185-191 
    Details
    ISSN: 1573-5036
    Keywords: carbon-labelling ; carbon dioxide production ; decomposition ; 14C-glucose ; Lemna ; soil organic matter ; sugars ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The duckweed Lemna gibba required light and a suitable energy source such as sucrose, glucose or fructose, for maximum growth in culture. The requirement for light was relatively unimportant and the plants grew well in a photon flux density of only 52 μmol m-2s-1 PAR. The uptake and incorporation of uniformly labelled 14C-glucose into fronds was related only to the concentration of the sugar. When incubated with soil, labelled L. gibba behaved in a manner similar to that of labelled ryegrass roots which had been produced by a more elaborate technique using a 14CO2 labelled atmosphere. During incubation with soil for 224 days the L. gibba material (specific activity 6133 Bq mg-1 d. wt) lost 64% of its radioactivity as 14CO2 and ryegrass (specific activity 6634 Bq mg-1 d. wt) lost 49%. Alkaline extracted humic and fulvic acids from soil had specific activities for the L. gibba incubation of 3409 and 407 Bq mg-1 solid and for ryegrass roots of 4609 and 546 Bq mg-1 solid respectively. The production of 13C or 14C-labelled L. gibba can be undertaken using only simple equipment producing material the specific radioactivity of which can be controlled by adjusting the activity of the sugar energy source.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00010144
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  • 42
    Electronic Resource
    Electronic Resource
    Seed colour assessment in Brassica napus using a Near Infrared Reflectance spectrometer adapted for visible light measurements (1994)
    Springer
    Euphytica 76 (1994), S. 45-51 
    Details
    ISSN: 1573-5060
    Keywords: Brassica napus ; light reflectance ; seed colour ; NIR
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary Improved oil, protein and fibre contents are associated with light seed colour in rapeseed but the lack of reliable and efficient methods to measure seed colour has hindered breeding efforts for this trait. The feasibility of using light reflectance to assess seed colour in Brassica napus was examined using scanning light reflectance spectrophotometry and near infrared reflectance (NIR). Light reflectance by seed samples from 30 doubled haploid (DH) lines segregating for seed colour increased as the wavelength of the illuminating light in the scanning spectrophotometer increased between 550 and 650 nm. The largest reflectance values were measured for the yellow seed samples; the brown seed samples were intermediate and the black seed samples had the lowest reflectance values. The areas under the reflectance curves were used to transform the spectra to single values. Average light reflectance area values for the seed colour classes were significantly different from each other. The DHs and their corresponding light reflectance area values were also used to calibrate a NIR analyzer modified with 670 and 710 nm filters. The best calibration curve used three wavelengths (670, 2190 and 2208 nm) and had a multiple correlation coefficient of 0.987. Light reflectance area values determined with the calibrated NIR analyzer for 30 randomly selected breeding lines could be used to categorize the colour of the seed samples with no discrepancies between the visual and instrument classifications. The results indicate that NIR can be used to assess seed colour in rapeseed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00024019
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  • 43
    Electronic Resource
    Electronic Resource
    A robust protocol for site-directed mutagenesis of the D1 protein inChlamydomonas reinhardtii: A PCR-splicedpsbA gene in a plasmid conferring spectinomycin resistance was introduced into apsbA deletion strain (1994)
    Springer
    Photosynthesis research 42 (1994), S. 121-131 
    Details
    ISSN: 1573-5079
    Keywords: chloroplast ; Photosystem II ; psbA ; site-directed mutagenesis ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In this paper, we describe a protocol to obtain a site-directed mutants in thepsbA gene ofChlamydomonas reinhardtii, which overcomes several drawbacks of previous protocols, and makes it possible to generate a mutant within a month. Since the large size of the gene, and the presence of four large introns has made molecular genetics of thepsbA gene rather unwieldy, we have spliced all of the exons of thepsbA gene by PCR to facilitate genetic manipulation and sequencing of the gene. The resultant construct (plasmid pBA153, with several unique restriction sites introduced at exon boundaries) carried 1.2 and 1.8 kb intact sequences from the 5′- and 3′-flanking regions, respectively. The plasmid was used to transform a D1-deletion mutant and was found to complement the deletion and restore photosynthetic activity. In addition, a bacterialaadA gene conferring spectinomycin resistance (spe r) was inserted downstream of the intron-freepsbA gene, to give construct pBA155. This allowed selection of mutant strains deficient in photosynthesis by using spectinomycin resistance, and eliminated the possibility of selection for revertant strains which is a consequence of having to use photosynthetic activity as a selection pressure. Finally, pBA155 was used to construct pBA157, in which additional restriction sites were inserted to facilitate cassette mutagenesis for generation of mutations in spans thought to be involved in donor-side interactions. AllpsbA deletion strains transformed with intron-freepsbA-aadA constructs encoding the wild-type D1 sequence, and screened on spectinomycin plates for thespe r phenotype, were able to grow photosynthetically, and all showed identical kinetics for electron transfer from primary (QA) to secondary quinone (QB) in Photosystem II, as assayed by the decay of the high fluorescence yield on oxidation of the reduced primary acceptor (QA −).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02187123
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  • 44
    Electronic Resource
    Electronic Resource
    Some features about transposition of the maize elementDissociation inNicotiana plumbaginifolia (1994)
    Springer
    Genetica 93 (1994), S. 41-48 
    Details
    ISSN: 1573-6857
    Keywords: Ac/Ds ; transformation ; transgenic plants ; transposon tagging
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have recently shown that a plasmid-borneDissociation (Ds) element can excise from extrachromosomal plasmid DNA and integrate into a plant genome in the presence of theActivator (Ac) transposase.Ds andAc-carrying plasmids were used to co-transformNicotiana plumbaginifolia protoplasts. Transgenic plants were regenerated and analyzed. Here we describe further characterization of the system and discuss its efficiency in terms of DNA transformation and transposon tagging.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01435238
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  • 45
    Electronic Resource
    Electronic Resource
    Transmission of injected DNA sequences to multiple eggs of Metaseiulus occidentalis and Amblyseius finlandicus (Acari: Phytoseiidae) following maternal microinjection (1994)
    Springer
    Experimental and applied acarology 18 (1994), S. 319-330 
    Details
    ISSN: 1572-9702
    Keywords: Maternal microinjection ; transformation ; genetic improvement
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The persistence of DNA injected into two species of adult female phytoseiids and its transmission to serial eggs deposited by them was assessed by the polymerase chain reaction (PCR). The effect of DNA concentration on persistence and transmission was examined in Metaseiulus occidentalis. M. occidentalis females were microinjected with plasmid DNA at three different concentrations (250, 500, 750 ng μL−1) and allowed to deposit one to five eggs before the females and their last eggs were analyzed. Plasmid DNA was found in 82% of the females assayed and in 70% of all the eggs analyzed (including the fifth eggs produced after microinjection). Transmission of DNA to multiple eggs was also examined in Amblyseius finlandicus. Females of this species are less traumatized by microinjection allowing analysis of transmission over a more extended number of eggs. Females were microinjected and allowed to deposit eggs until their death. DNA from every fifth egg was analyzed by the PCR. PCR products were amplified from 51% of the eggs and from all egg classes except the 30th egg. The persistence and presence of plasmid DNA in both eggs and females suggests that (1) maternal microinjection is a more efficient method for DNA delivery than traditional egg microinjection, (2) it may be possible to isolate transformants from fewer maternally-microinjected females than originally expected, and (3) maternal microinjection could be useful as a DNA delivery system in other phytoseiids.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00116313
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  • 46
    Electronic Resource
    Electronic Resource
    Genetics and gibberellin production inGibberella fujikuroi (1994)
    Springer
    Antonie van Leeuwenhoek 65 (1994), S. 217-225 
    Details
    ISSN: 1572-9699
    Keywords: Gibberella fujikuroi ; gibberellins ; mutants ; regulation by nitrogen ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Gibberella fujikuroi (Fusarium moniliforme) is a complex group of plant pathogens. Some strains produce gibberellic acid and other gibberellins that promote growth and regulate various stages in plant development. The paper describes the research effort directed to development of genetic tools for this species. Furthermore the main features of the gibberellin biosynthetic pathway as established in Gibberella are described.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00871950
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  • 47
    Electronic Resource
    Electronic Resource
    Influence of the triazole growth retardant BAS 111..W on phytohormone levels in senescing intact pods of oilseed rape (1994)
    Springer
    Plant growth regulation 14 (1994), S. 115-118 
    Details
    ISSN: 1573-5087
    Keywords: abscisic acid ; 1-aminocyclopropane-1-carboxylic acid ; BAS 111..W ; Brassica napus ; cytokinins ; oilseed rape ; pod ; senescence ; triazole growth retardant
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Foliar treatment of oilseed rape plants (Brassica napus L.ssp. napus cv. Linetta) with the growth retardant BAS 111..W at the 5th leaf stage delayed pod senescence during early maturation. Changes of immunoreactive cytokinin- and abscisic acid (ABA)- like substances and of the ethylene precursor 1-aminocyclo-propane-1-carboxylic acid (ACC) and its malonyl-conjugate (MACC) were determined in intact whole pods. When compared with control plants, higher levels of total chlorophyll correlated with four-fold and three-fold increases of trans-zeatin riboside- and dihydrozeatin riboside-type cytokinins, respectively, in the pods of plants treated with 0.25 mg BAS 111..W per plant. Isopentenyladenosine-type cytokinins and ACC and MACC contents remained virtually unchanged, whereas ABA levels dropped considerably below those of controls (60% reduction). However, when analysed at late pod maturity, BAS 111..W treatment no longer affected the total chlorophyll content, or the levels of cytokinins, ABA, ACC and MACC. We hypothesize that the retardant-induced changes in the hormonal status of the pods, favouring the senescence-delaying cytokinins as opposed to abscisic acid, could contribute to the developmental delay.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00025211
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  • 48
    Electronic Resource
    Electronic Resource
    Self-incompatibility as a pollination control mechanism for spring oilseed rape, Brassica napus L. (1994)
    Springer
    Euphytica 75 (1994), S. 27-30 
    Details
    ISSN: 1573-5060
    Keywords: Brassica napus ; heterosis ; hybrid breeding ; oilseed rape ; self-incompatibility ; pollination control
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary Self-incompatibility was shown to be an effective method of pollination control in spring rapeseed (B. napus L. ssp. oleifera (Metzg.)) by comparing the yield of a Westar-Topas syn-1 produced by crossing two SI lines with the yield of the corresponding syn-1 produced by hand pollination. Although the trial showed high-parent heterosis in the syn-1s, there was insufficient replication to determine the level of heterosis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00024528
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  • 49
    Electronic Resource
    Electronic Resource
    Stably transformed cell lines from protoplasts of maize endosperm suspension cultures (1994)
    Springer
    Plant cell, tissue and organ culture 37 (1994), S. 39-46 
    Details
    ISSN: 1573-5044
    Keywords: endosperm cell culture ; maize ; protoplast ; transformation ; zeins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Protoplasts were isolated from Zea mays (L.) A69Y endosperm suspension cultures and transformed by polyethylene glycol mediated DNA uptake with chimaeric gene constructs containing β-glucuronidase (GUS) or neomycin phosphotransferase II (NPTII); GUS-expressing and Kanamycin-resistant cultures were recovered. The transformed cells showed integration of the introduced foreign genes into genomic DNA and maintained their ability to synthesize endosperm-specific reserve proteins (zeins). No deletion or rearrangement of zein genes were observed in transformed cultures. Stable transformation of cultured maize endosperm cells may therefore represent a new methodological approach for the study of the transcriptional regulation of endosperm-expressed genes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00048115
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  • 50
    Electronic Resource
    Electronic Resource
    Efficient plant regeneration through somatic embryogenesis from callus induced on mature rice embryos (Oryza sativa L.) (1994)
    Springer
    Plant cell, tissue and organ culture 36 (1994), S. 259-264 
    Details
    ISSN: 1573-5044
    Keywords: monocotyledons ; Oryza sativa L. ; plant regeneration ; rice ; somatic embryogenesis ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract To obtain a reproducible efficient procedure for regeneration of rice plants through somatic embryogenesis from callus four published methods of callus induction and regeneration were compared. Callus was initiated from mature embryos of the Japonica cultivar Taipei 309 of rice (Oryza sativa L.). The number, mass and morphology of the callus formed on the scutellum were dependent on the medium used. A limited humidity and an optimal aeration of the culture vessels enhanced the frequency of embryogenesis and plant regeneration. A method described by Poonsapaya et al. (1989) was found to be the most efficient and was slightly modified. As a result 98% of the T309 embryos formed callus, of which 63% regenerated into plants. Each callus yielded an average of 6 plants. Plant morphology, fertility and seed set of the regenerants were found to be normal.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00037729
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  • 51
    Electronic Resource
    Electronic Resource
    Factors that effect leaf regeneration efficiency in apple, and effect of antibiotics in morphogenesis (1994)
    Springer
    Plant cell, tissue and organ culture 37 (1994), S. 257-269 
    Details
    ISSN: 1573-5044
    Keywords: adventitious shoots ; Malus x domestica Borkh. ; tissue culture ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Several factors that affect the frequency of organogenesis in apple leaf explants were examined for the scion cultivars ‘Empire’, ‘Freedom’, ‘Golden Delicious’, ‘Liberty’, ‘McIntosh’, and ‘Mutsu’ and for the rootstocks Malling 7A and Malling 26. The main factors affecting morphogenesis were BA concentration, basal medium, leaf explant origin and maturity, explant orientation, and photosynthetic photon flux. Depending on the genotype, optimal regeneration was obtained using either 22.2 or 31.1 μM BA and the N6 basal medium, with the exception of ‘Golden Delicious’ which regenerated better on MS medium. After 6 weeks, the average number of shoots per segment varied from 5 to 16, and the percentage of regeneration between 70 and 100%, depending on the genotype tested and the maturity of the explant. Regeneration capacity increased dramatically from the tip towards the base of the leaf, and was higher from the middle to the proximal end. Cefotaxime and carbenicillin, two antibiotics commonly used during transformation studies to eliminate Agrobacterium tumefaciens from plant tissue, were tested to determine their effect on morphogenesis. Cefotaxime at a dose of 250 mg 1-1 enhanced regeneration and shoot development, whereas carbenicillin at a dose of 500 mg l-1 induced abundant callus formation and inhibited regeneration. Kanamycin, a widely used selection agent for plant transformation, strongly inhibited regeneration even at very low doses. Schemes for selection and recovery of transgenic apple plants when kanamycin is used as the selection agent are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00042339
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  • 52
    Electronic Resource
    Electronic Resource
    Efficient production of doubled haploid Brassica napus plants by colchicine treatment of microspores (1994)
    Springer
    Euphytica 75 (1994), S. 95-104 
    Details
    ISSN: 1573-5060
    Keywords: Brassica napus ; microspore culture ; colchicine treatment ; chromosome doubling ; DH-breeding
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary The effect of colchicine on isolated microspore cultures of Brassica napus was evaluated in order to combine a positive effect of colchicine on the induction of embryogenesis with the possibility to induce chromosome doubling at an early developmental stage, thus avoiding the production of haploid or chimeric plants. Colchicine was added to the culture medium immediately after isolation of B. napus microspores. The cultures were incubated from 6 to 72 h with various concentrations of colchicine. Samples were taken from the regenerating embryoids after 6 weeks for ploidy determination by flow-cytometry. The highest diploidization rate was obtained after a 24 h treatment of microspores with 50 mg/l colchicine, leading to 80–90% diploid embroids. A concentration of 100 mg/l colchicine applied for the same duration resulted in a lower diploidization rate (76–80%). Treatment durations of 6 h were not long enough to induce a high rate of diploidization, whereas the application of 10 mg/l for 72 h was also very effective. A sample of the plants regenerated from the colchicine treated microspores was transferred to the greenhouse. The plants looked similar to normal diploid rapeseed plants and showed reasonable pod and seed set. Thus, an additional generation for seed increase in the greenhouse is rendered unnecessary. The advantage of applying a minimum volume of colchicine under controlled in vitro conditions means a considerable saving of time and labour in DH-breeding programs.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00024536
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  • 53
    Electronic Resource
    Electronic Resource
    Micropropagation of thirteen Malus cultivars and rootstocks, and effect of antibiotics on proliferation (1994)
    Springer
    Plant growth regulation 15 (1994), S. 55-67 
    Details
    ISSN: 1573-5087
    Keywords: apple (Malus × domestica Borkh.) ; selection ; tissue culture ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Several factors that affect in vitro establishment, proliferation, and rooting of thirteen Malus cultivars and rootstocks were studied. Apple shoot tips (1.5±0.5 cm in length) were established using ascorbic and citric acids as antioxidants. Four proliferation media containing 1.0 mg 1−1 BA and different concentrations of IBA and GA3 were tested. Proliferation rates varied depending on the genotype and medium used. The highest proliferation rate was obtained for a rootstock that produced 11.6±2.5 shoots (1.5±0.8 cm in length) per tube per month. Rooting was induced with IBA for all the genotypes tested. The optimal IBA concentration was cultivar dependent (between 0.1 and 1.0 mg 1−1 IBA), and lower concentrations were necessary to induce rooting in liquid rather than in solid medium. The effects on shoot-tip proliferation of cefotaxime, carbenicillin and kanamycin, three antibiotics commonly used for transformation studies, were also evaluated. Cefotaxime at 200 mg 1−1 stimulated shoot growth and development, but at 500 mg 1−1 caused abnormal shoot morphology. Carbenicillin at 500 mg 1−1, alone or in combination with cefotaxime at 200 mg 1−1, inhibited proliferation and caused excessive enlargement of the basal leaves, inducing callus formation and release of phenolic compounds in the medium. Kanamycin at 50 mg 1−1 was phytotoxic and caused shoot chlorosis and necrosis. Consideration of the toxicity of these antibiotics is critical when designing transformation schemes for selection and recovery of transgenic apple plants.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00024677
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  • 54
    Electronic Resource
    Electronic Resource
    Solution structure of a core peptide derived from scyllatoxin (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 205-215 
    Details
    ISSN: 0887-3585
    Keywords: peptide folding ; disulfide framework ; insect toxins ; NMR ; distance geometry ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An analysis of the sequences of scyllatoxin and charybdotoxin suggested that it would be possible to design a core peptide sequence which would still fold to give the β-hairpin and helix seen in the toxins, but which would eliminate one disulfide and connecting residues. The core sequence was modeled, then synthesized and purified. The cysteines oxidize in air to give the same disulfide pairings as seen in the parent toxins as the major product. The three-dimensional structure of the core sequence peptide, termed Max, was determined using proton NMR spectroscopy and found to be identical in secondary structure to the toxins. However differences were found in the relative orientation of the β-hairpin and helix. The use of this structural motif, found in many insect toxins, as a disulfide framework for exploring sequence/structure/activity relationships is discussed. © 1994 John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180302
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  • 55
    Electronic Resource
    Electronic Resource
    Thermodynamics of ubiquitin unfolding (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 246-253 
    Details
    ISSN: 0887-3585
    Keywords: microcalorimetry ; heat capacity ; enthalpy ; hydrogen bonding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The energetics of ubiquitin unfolding have been studied using differential scanning microcalorimetry. For the first time it has been shown directly that the enthalpy of protein unfolding is a nonlinear function of temperature. Thermodynamic parameters of ubiquitin unfolding were correlated with the structure of the protein. The enthalpy of hydrogen bonding in ubiquitin was calculated and compared to that obtained for other proteins. It appears that the energy of hydrogen bonding correlates with the average length of the hydrogen bond in a given protein structure. © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180305
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  • 56
    Electronic Resource
    Electronic Resource
    Hydrogen bond strength and β-sheet propensities: The role of a side chain blocking effect (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 262-266 
    Details
    ISSN: 0887-3585
    Keywords: protein structure prediction ; protein stability ; hydrogen bond ; β-sheet ; amino acid propensity ; steric effect ; hydrogen exchange ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Amino acid side chains can enhance peptide group hydrogen bond strength in protein structures by obstructing the competing hydrogen bond to solvent in the unfolded state. Available data indicate that the steric blocking effect contributes an average of 0.5 kJ per residue to protein hydrogen bond strength and accounts for the intrinsic α-sheet propensities of the amino acids. In available data for helical models, the contribution to α-helix propensities is obscured especially by large context-dependent effects. These issues are all related by a common side chain-dependent steric clash which disfavors peptide to water H-bond formation, peptide to catalyst complexation in hydrogen exchange reactions (Bai et al., Proteins 17:75-86, 1993), and peptide to peptide H-bonding in the helical main chain conformation (Creamer and Rose, Proc. Natl. Acad. Sci. U.S.A. 89:5937-5941, 1992) but not in α-strands. © 1994 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340180307
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    A method for α-helical integral membrane protein fold prediction (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 281-294 
    Details
    ISSN: 0887-3585
    Keywords: membrane ; protein ; structure ; prediction ; G-protein coupled receptor ; rhodopsin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Integral membrane proteins (of the α-helical class) are of central importance in a wide variety of vital cellular functions. Despite considerable effort on methods to predict the location of the helices, little attention has been directed toward developing an automatic method to pack the helices together. In principle, the prediction of membrane proteins should be easier than the prediction of globular proteins: there is only one type of secondary structure and all helices pack with a common alignment across the membrane. This allows all possible structures to be represented on a simple lattice and exhaustively enumerated. Prediction success lies not in generating many possible folds but in recognizing which corresponds to the native. Our evaluation of each fold is based on how well the exposed surface predicted from a multiple sequence alignment fits its allocated position. Just as exposure to solvent in globular proteins can be predicted from sequence variation, so exposure to lipid can be recognized by variable-hydrophobic (variphobic) positions. Application to both bacteriorhodopsin and the eukaryotic rhodopsin/opsin families revealed that the angular size of the lipid-exposed faces must be predicted accurately to allow selection of the correct fold. With the inherent uncertainties in helix prediction and parameter choice, this accuracy could not be guaranteed but the correct fold was typically found in the top six candidates. Our method provides the first completely automatic method that can proceed from a scan of the protein sequence databanks to a predicted three-dimensional structure with no intervention required from the investigator. Within the limited domain of the seven helix bundle proteins, a good chance can be given of selecting the correct structure. However, the limited number of sequences available with a corresponding known structure makes further characterization of the method difficult. © 1994 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180309
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    Crystallization and preliminary crystallographic studies of the precursor and mature forms of a neutral lipase from the fungus Rhizopus delemar (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 301-306 
    Details
    ISSN: 0887-3585
    Keywords: triglyceride lipase ; proenzyme ; molecular replacement ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A neutral lipase from the filamentous fungus Rhizopus delemar has been crystallized in both its proenzyme and mature forms. Although the latter crystallizes readily and produces a variety of crystal forms, only one was found to be suitable for X-ray studies. It is monoclinic (C2, a = 92.8 Å, b = 128.9 Å, c = 78.3 Å, β = 135.8) with two molecules in the asymmetric unit related by a noncrystallographic diad. The prolipase crystals are orthorhombic (P212121, with a = 79.8 Å, b = 115.2 Å, c = 73.0 Å) and also contain a pair of molecules in the asymmetric unit. Initial results of molecular replacement calculations using the refined coordinates of the related lipase from Rhizomucor miehei identified the correct orientations and positions of the protein molecules in the unit cells of crystals of both proenzyme and the mature form. © 1994 John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180311
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    Correlated mutations and residue contacts in proteins (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 309-317 
    Details
    ISSN: 0887-3585
    Keywords: protein structure prediction ; predicted contact maps ; correlated mutations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The maintenance of protein function and structure constrains the evolution of amino acid sequences. This fact can be exploited to interpret correlated mutations observed in a sequence family as an indication of probable physical contact in three dimensions. Here we present a simple and general method to analyze correlations in mutational behavior between different positions in a multiple sequence alignment. We then use these correlations to predict contact maps for each of 11 protein families and compare the result with the contacts determined by crystallography. For the most strongly correlated residue pairs predicted to be in contact, the prediction accuracy ranges from 37 to 68% and the improvement ratio relative to a random prediction from 1.4 to 5.1. Predicted contact maps can be used as input for the calculation of protein tertiary structure, either from sequence information alone or in combination with experimental information. © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180402
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    Analysis of Cα geometry in protein structures (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 324-337 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; secondary structure ; peptide geometry ; Ramachandran plot ; β-turns ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The polypeptide of a protein molecule can be considered as a chain of Cα atoms linked by pseudobonds between the Cα atoms of successive amino acid residues. This paper presents an analysis of the angle and dihedral angles made by these pseudobonds in protein structures determined at high resolution by X-ray crystallography. This analysis reveals a strong correlation between Cα geometry and the protein fold. The regular features of protein secondary structure such as α-helix and α-sheet are very clearly defined. In addition, it is possible to identify with some confidence the discrete populations of particular conformations of α-turn. Comparison with the traditional Ramachandran type of plot demonstrates that an analysis of protein structure on the basis of Cα geometry provides a richer description of protein conformation. In addition, the characteristics of this geometry could be a useful guide in model building of protein structure. © 1994 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340180404
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    Crystallization of a fragment of human fibronectin: Introduction of methionine by site-directed mutagenesis to allow phasing via selenomethionine (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 48-54 
    Details
    ISSN: 0887-3585
    Keywords: X-ray crystallography ; extracellular matrix ; multiwavelength anomalous diffraction (MAD) ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of a fragment of human fibronectin encompassing the 7th through the RGD-containing 10th type III repeats (FN7-10) have been produced with protein expressed in E. coli. The crystals are monoclinic with one molecule in the asymmetric unit and diffract to beyond 2.0 Å Bragg spacings. A mutant FN7-10 was produced in which three methionines, in addition to the single native methionine already present, have been introduced by site-directed mutagenesis. Diffraction-quality crystals of this mutant protein have been grown in which methionine was replaced with selenomethionine. The introduction of methionine by site-directed mutagenesis to allow phasing from selenomethionyl-substituted crystals is shown to be feasible by this example and is proposed as a general approach to solving the crystallographic phase problem. Strategies for selecting propitious sites for methionine mutations are discussed. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190107
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    Combining evolutionary information and neural networks to predict protein secondary structure (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 55-72 
    Details
    ISSN: 0887-3585
    Keywords: secondary structure prediction ; prediction of secondary structure class ; prediction of secondary structure content ; evolutionary information ; multiple alignment profiles ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Using evolutionary information contained in multiple sequence alignments as input to neural networks, secondary structure can be predicted at significantly increased accuracy. Here, we extend our previous three-level system of neural networks by using additional input information derived from multiple alignments. Using a position-specific conservation weight as part of the input increases performance. Using the number of insertions and deletions reduces the tendency for overprediction and increases overall accuracy. Addition of the global amino acid content yields a further improvement, mainly in predicting structural class. The final network system has a sustained overall accuracy of 71.6% in a multiple cross-validation test on 126 unique protein chains. A test on a new set of 124 recently solved protein structures that have no significant sequence similarity to the learning set confirms the high level of accuracy. The average cross-validated accuracy for all 250 sequence-unique chains is above 72%. Using various data sets, the method is compared to alternative prediction methods, some of which also use multiple alignments: the performance advantage of the network system is at least 6 percentage points in three-state accuracy. In addition, the network estimates secondary structure content from multiple sequence alignments about as well as circular dichroism spectroscopy on a single protein and classifies 75% of the 250 proteins correctly into one of four protein structural classes. Of particular practical importance is the definition of a position-specific reliability index. For 40% of all residues the method has a sustained three-state accuracy of 88%, as high as the overall average for homology modelling. A further strength of the method is greatly increased accuracy in predicting the placement of secondary structure segments. © 1994 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190108
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    Expression, purification, and crystallization of restriction endonuclease PvuII with DNA containing its recognition site (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 77-79 
    Details
    ISSN: 0887-3585
    Keywords: endonuclease overexpression ; crystallization ; X-ray diffraction ; protein-DNA complex ; Type II restriction enzyme ; vapor diffusion ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have overexpressed the type II restriction endonuclease PvuII (R.PvuII) in E. coli, prepared large amounts of the homogeneous enzyme, and crystallized it with an oligonucleotide carrying a PvuII recognition site. The cocrystals are orthorhombic space group P212121 with cell constants a = 95.8 Å, b = 86.3 Å, c = 48.5 Å, and diffract X-rays to at least 2.7 Å. There is a complex of two protein subunits and one oligonucleotide duplex in the asymmetric unit. © 1994 Wiley-Liss, Inc.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190110
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    Masthead (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190201
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    Crystallization and preliminary X-ray crystallographic analysis of phospholipid transfer protein from maize seedlings (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 80-83 
    Details
    ISSN: 0887-3585
    Keywords: maize protein ; crystals ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Phospholipid transfer protein from maize seedlings has been crystallized using trisodium citrate as precipitant. The crystal belongs to the orthorhombic space group P212121 with unit cell dimensions of a = 24.46 Å, b = 49.97 Å, and c = 69.99 Å. The presence of one molecule in the asymmetric unit gives a crystal volume per protein mass (Vm) of 2.36 Å 3/Da and a solvent content of 48% by volume. The X-ray diffraction pattern extends at least to 1.6 Å Bragg spacing when exposed to both CuKα and synchrotron X-rays. A set of X-ray data to approximately 1.9 Å Bragg spacing has been collected from a native crystal. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190111
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    α-Helix-forming propensities in peptides and proteins (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 85-97 
    Details
    ISSN: 0887-3585
    Keywords: protein conformation ; secondary structure ; protein folding ; helix stability ; helix formation ; conformational entropy ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Much effort has been invested in seeking to understand the thermodynamic basis of helix stability in both peptides and proteins. Recently, several groups have measured the helix-forming propensities of individual residues (Lyu, P. C., Liff, M. I., Marky, L. A., Kallenbach, N. R. Science 250:669-673, 1990; O'Neil, K. T., DeGrado, W. F. Science 250:646-651, 1990; Padmanabhan, S., Marqusee, S., Ridgeway, T., Laue, T. M., Baldwin, R. L. Nature (London) 344:268-270, 1990). Using Monte Carlo computer simulations, we tested the hypothesis that these differences in measured helix-forming propensity are due primarily to loss of side chain conformational entropy upon helix formation (Creamer, T. P., Rose, G. D. Proc. Natl. Acad. Sci. U.S.A. 89:5937-5941, 1992). Our previous study employed a rigid helix backbone, which is here generalized to a completely flexible helix model in order to ensure that earlier results were not a methodological artifact. Using this flexible model, side chain rotamer distributions and entropy losses are calculated and shown to agree with those obtained earlier. We note that the side chain conformational entropy calculated for Trp in our previous study was in error; a corrected value is presented. Extending earlier work, calculated entropy losses are found to correlate strongly with recent helix propensity scales derived from substitutions made within protein helices (Horovitz, A., Matthews, J. M., Fersht, A. R. J. Mol. Biol. 227:560-568, 1992; Blaber, M., Zhang, X.-J., Matthews, B. M. Science 260:1637-1640, 1993). In contrast, little correlation is found between these helix propensity scales and the accessible surface area buried upon formation of a model polyalanyl α-helix. Taken in sum, our results indicate that loss of side chain entropy is a major determinant of the helix-forming tendency of residues in both peptide and protein helices. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190202
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    1.56 Å structure of mature truncated human fibroblast collagenase (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 98-109 
    Details
    ISSN: 0887-3585
    Keywords: crystallography ; hydroxamate ; high resolution ; metalloproteinase ; zinc ; X-ray ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The X-ray crystal structure of a 19 kDa active fragment of human fibroblast collagenase has been determined by the multiple isomorphous replacement method and refined at 1.56 Å resolution to an R-factor of 17.4%. The current structure includes a bound hydroxamate inhibitor, 88 waters and three metal atoms (two zincs and a calcium). The overall topology of the enzyme, comprised of a five stranded β-sheet and three α-helices, is similar to the thermolysin-like metalloproteinases. There are some important differences between the collagenase and thermolysin families of enzymes. The active site zinc ligands are all histidines (His-218, His-222, and His-228). The presence of a second zinc ion in a structural role is a unique feature of the matrix metalloproteinases. The binding properties of the active site cleft are more dependent on the main chain conformation of the enzyme (and substrate) compared with thermolysin. A mechanism of action for peptide cleavage similar to that of thermolysin is proposed for fibroblast collagenase. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190203
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    Kinetic study on myoglobin refolding monitored by five optical probe stopped-flow methods (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 110-119 
    Details
    ISSN: 0887-3585
    Keywords: folding intermediate ; urea denaturation ; stopped-flow circular dichroism ; molten globule ; hemindicyanide ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The refolding kinetics of horse cyanometmyoglobin induced by concentration jump of urea was investigated by five optical probe stopped-flow methods: absorption at 422 nm, tryptophyl fluorescence at around 340 nm, circular dichroism (CD) at 222 nm, CD at 260 nm, and CD at 422 nm. In the refolding process, we detected three phases with rate constants of 〉 1 × 102 s-1, (4.5-9.3) S-1, and (2-5) × 10-3 s-1. In the fastest phase, a substantial amount of secondary structure (40%) is formed within the dead time of the CD stopped-flow apparatus (10.7 ms). The kinetic intermediate populated in the fastest phase is shown to capture a hemindicyanide, suggesting that a “heme pocket precursor” recognized by hemindicyanide must be constructed within the dead time. In the middle phase, most of secondary and tertiary structures, especially around the captured hemindicyanide, have been constructed. In the slowest phase, we detected a minor structural rearrangement accompanying the ligand-exchange reaction in the fifth coordination of ferric iron. We present a possible model for the refolding process of myoglobin in the presence of the heme group. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190204
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    Decoupling of melting domains in immobilized ribonuclease A (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 120-131 
    Details
    ISSN: 0887-3585
    Keywords: enzymes ; protein immobilization ; microcalorimetry ; protein melting domains ; protein DSC ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Ribonuclease A has been immobilized on silica beads through glutaraldeyde-mediated chemical coupling in order to improve the stability of the protein against thermal denaturation. The thermodynamic and binding properties of the immobilized enzyme have been studied and compared with those of the free enzyme. The parameters describing the binding of the inhibitor 3′ -CMP (Ka and ΔH) as monitored by spectrophotometry and calorimetry were not significantly affected after immobilization. Conversely both the stability and unfolding mechanism drastically changed. Thermodynamic analysis of the DSC data suggests that uncoupling of protein domains has occurred as a consequence of the immobilization. The two state approximation of the protein unfolding process is not longer valid for the immobilized RNase. Protein stability strongly depends on the hydrophobicity properties of the support surface as well as on the presence of the inhibitor and pH. For example, after immobilization on a highly hydrophobic surface, the enzyme is partially in the unfolded state. The binding of a ligand is able to reorganize the protein structure into a native-like conformation. The refolding rates are different for the two protein domains and vary as a function of pH and presence of the inhibitor 3′-CMP. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190205
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    Temperature-induced complementarity as a mechanism for biomolecular assembly (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 73-76 
    Details
    ISSN: 0887-3585
    Keywords: molecular recognition ; protein assembly ; protein folding ; protein interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Recent advances in the measurement and theory of “hydration” interactions between biomolecules provide a basis on which to formulate mechanisms of biomolecular recognition. In this paper we have developed a mathematical formalism for analyzing specificity encoded in dynamic distributions of surface polar groups, a formalism that incorporates newly recognized properties of directly measured “hydration” forces. As expected, attraction between surfaces requires complementary patterns of surface polar groups. In contrast to usual expectations, thermal motion can create these complementary surface configurations. We have demonstrated that assembly can occur with an increase in conformational entropy of polar residues. Elevated temperature then facilitates recognition rather than hinders it. This mechanism might underlie some temperature-favored assembly reactions common in biological systems that are usually associated with the “hydrophobic effect” only. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190109
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    Coiled-coil stutter and link segments in keratin and other intermediate filament molecules: A computer modeling study (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 174-184 
    Details
    ISSN: 0887-3585
    Keywords: coiled-coils ; keratin ; intermediate filament proteins ; link segments ; heptad phasing ; computer modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structural discontinuities have previously been identified in four regions of the coiled-coil rod domain structure present in intermediate filament (IF) protein molecules. These include a point at which a phase shift occurs in the heptad periodicity characteristic of the sequence of polar and apolar residues in α-helical coiled-coils, and three links that lack a heptad substructure. We have studied these regions by computer-based molecular modeling and comparative sequence analysis and conclude that the phasing discontinuity can be accommodated without significant distortion of the overall double-helical chain conformation; the L2 link has a similar conformation in all different types of IF molecules, a favorable conformation being one in which the two strands wrap tightly around each other; the L12 links vary in length between different IF types but contain important sequence similarities suggestive of a partial β structure; the L1 links show larger variations in length, a lower degree of similarity, and probably diverse structures. Variations in the overall charges of the different links suggest that ionic interactions may playa significant role in filament assembly. The results also have general significance for other α-fibrous proteins in which either the characteristic heptad phasing undergoes a discontinuity or where a short non-coiled-coil sequence occurs within a coiled-coil rod domain structure. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340200207
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    Crystallization and characterization of the recombinant human Clara cell 10-kDa protein (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 191-196 
    Details
    ISSN: 0887-3585
    Keywords: human Clara cell 10-kDa protein ; X-ray diffraction ; phospholipase A2 inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of recombinant human Clara cell 10-kDa protein were grown both from ammonium sulfate and polyethylene glycol (PEG) solutions. Crystals grown from ammonium sulfate solution have been characterized by X-ray diffraction studies as monoclinic with the space group C2 and lattice constants a = 69.2 Å, b = 83.0 Å, c = 58.3 Å, and β = 99.7°. The monoclinic crystals diffract to beyond 2.5 Å. Some of the crystals grown from PEG were of a similar habit to those grown from ammonium sulfate, but others were triclinic with the space group P1 and cell constants a = 40.3 Å, b = 46.3 Å, c = 51.3 Å, α = 117.7°, β = 102.3°, and γ = 71.4°. These crystals diffract to beyond 3.2 Å. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340200209
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    Conformational analysis of hemopexin by fourier-transform infrared and circular dichroism spectroscopy (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 185-190 
    Details
    ISSN: 0887-3585
    Keywords: heme ; secondary structure ; conformation ; hemopexin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Hemopexin is a serum glyco-protein that binds heme with the highest known affinity of any characterized heme-binding protein and plays an important role in receptormediated cellular heme uptake. Complete understanding of the function of hemopexin will require the elucidation of its molecular structure. Previous analysis of the secondary structure of hemopexin by far-UV circular dichroism (CD) failed due to the unusual positive ellipticity of this protein at 233 nm. In this paper, we present an examination of the structure of hemopexin by both Fourier-transform infrared (FTIR) and circular dichroism spectroscopy. Our studies show that hemopexin contains about 55% β-structure, 15% α-helix, and 20% turns. The two isolated structural domains of hemopexin each have secondary structures similar to hemopexin. Although there are significant tertiary conformational changes indicated by the CD spectra, the overall secondary structure of hemopexin is not affected by binding heme. However, moderate changes in secondary structure do occur when the heme-binding domain of hemopexin associates with heme. In spite of the exceptionally tight binding at neutral pH, heme is released from the bis-histidyl heme-hemopexin complex at pH 5.0. Under this acidic condition, hemopexin maintains the same overall secondary structure as the native protein and is able to resume the heme-binding function and the native structure of the hemeprotein (as indicated by the CD spectra) when returned to neutral pH. We propose that the state of hemopexin identified in vitro at pH 5.0 resembles that of this protein in the acidic environment of the endosomes in vivo when hemopexin releases heme during receptor-mediated endocytosis. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340200208
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    Masthead (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340200301
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    Preliminary crystallographic analysis of an enzyme involved in erythromycin biosynthesis: Cytochrome P450eryF (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 197-201 
    Details
    ISSN: 0887-3585
    Keywords: cytochrome P450 ; erythromycin ; P450eryF ; crystallization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Cytochrome P450eryF was overexpressed in Escherichia coli and purified in high yield. Crystals of the protein in the presence of the substrate, 6-deoxyerythronolide B, have been obtained by the hanging drop vapor diffusion method, using polyethylene glycol 4000 as a precipitant. The crystals belong to the orthorhombic space group P212121 with unit cell dimensions of a = 54.16 Å, b = 79.67 Å, and c = 99.48 Å and one molecule per asymmetric unit. A complete native data set has been collected to a resolution of 2.1 Å, and anomalous dispersion difference Patterson maps have revealed the location of the single heme iron atom. © 1994 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200210
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    Homology modeling of the Abl-SH3 domain (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 203-215 
    Details
    ISSN: 0887-3585
    Keywords: SH3 ; Abl ; molecular modeling ; homology modeling ; molecular dynamics ; protein structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A tertiary structure model of the Abl-SH3 domain is predicted by using homology modeling techniques coupled to molecular dynamics simulations. Two template proteins were used, Fyn-SH3 and Spc-SH3. The refined model was extensively checked for errors using criteria based on stereochemistry, packing, solvation free-energy, accessible surface areas, and contact analyses. The different checking methods do not totally agree, as each one evaluates a different characteristic of protein structures. Several zones of the protein are more susceptible to incorporating errors. These include residues 13, 15, 35, 39, 45, 46, 50, and 60. An interesting finding is that the measurement of the Cα chirality correlated well with the rest of the criteria, suggesting that this parameter might be a good indicator of correct local conformation. Deviations of more than 4 degrees may be indicative of poor local structure. © 1994 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200302
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    Homologous modeling of the lysosomal protective protein/carboxypeptidase L: Structural and functional implications of mutations identified in galactosialidosis patients (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 81-93 
    Details
    ISSN: 0887-3585
    Keywords: serine carboxypeptidase ; protein modeling ; mutation analysis ; comparative modeling ; cathepsin A ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The deficiency of the lysosomal protective protein/carboxypeptidase L (CARB L) causes the lysosomal storage disorder, galactosialidosis, characterized by neuraminidase and β-galactosidase deficiencies in patients' cells. The three enzymes form a complex inside the lysosome, and the neuraminidase and β-galactosidase deficiencies are secondary to CARB L deficiency. Sequence similarity and common enzymological properties suggest that the protomeric tertiary structure of CARB L is conserved within a family of serine carboxypeptidases which includes the yeast carboxypeptidase Y, killer expression I gene product and several plant carboxypeptidases. We used this homology to build a model of the CARB L structure based on the recently published X-ray atomic coordinates of the wheat carboxypeptidase II (CPDW-II) which shares 32% primary structure identity with CARB L. Small insertions and deletions were accommodated into the model structure by energy minimization using the DREIDING II force field. The Cα atomic-coordinates of the final CARB L model have a RMS shift of 1.01 Å compared to the corresponding conserved residues in the CPDW-II template structure. The correct orientation of the homologous catalytic triad residues Ser150, His429 and Asp392, the potential energy calculations and the distribution of hydrophobic and hydrophillic residues in the structure all support the validity of the CARB L model. Most missense mutations identified in galactosialidosis patients were located in secondary structural elements except for the Tyr211→Asn mutation which is in a loop. The other mutant residues have their side chains deeply buried in the central β-sheet of the model structure except for the Phe412→Val mutation which is located in the dimer interface. The predicted effects of specific mutations on CARB L structural stability correlates well with recently published transient expression studies of mutant CARB L (Shimmoto, M. et al., J. Clin. Invest., 91:2393-2399, 1993). © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180110
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    Protein simulations using techniques suitable for very large systems: The cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 227-247 
    Details
    ISSN: 0887-3585
    Keywords: cell multipole method ; Newton-Euler inverse mass operator ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Two new methods developed for molecular dynamics simulations of very large proteins are applied to a series of proteins ranging up to the protein capsid of tomato bushy stunt virus (TBSV).For molecular dynamics of very large proteins and polymers, it is useful to carry out the dynamics using internal coordinates (say, torsions only) rather than Cartesian coordinates. This allows larger time steps, eliminates problems with the classical description of high energy modes, and focuses on the important degrees of freedom. The resulting equation of motion has the form where for T is the vector of generalized forces, M(θ) is the moments of inertia tensor, is the vector of torsions, and C is a vector containing Coriolis forces and nonbond forces. The problem is that to calculate the acceleration vector from M, C, and Trequires inverting. M(θ), an order N3calculation. Since the number of degrees of freedom might be 300,000 for a million atom system, solving these equations every time step is impractical, restricting internal coordinate methods to small systems. The new method, Newton-Euler Inverse Mass Operator (NEIMO) dynamics, constructs the torsional accelerations vector directly by an order N process, allowing internal-coordinate dynamics to be solved for super larger (million atom) systems, The first use of the NEIMO method for molecular dynamics of proteins is presented here.A second serious difficulty for large proteins is calculation of the nonbond forces. We report here the first application to proteins of the new Cell Multipole Method (CMM) to evaluate the Coulomb and van der Waals interactions. The cost of CMM scales linearly with the number of particles while retaining an accuracy significantly better than standard non bond methods (involving cutoffs).Results for NEIMO and CMM are given for simulations of a wide range of peptide and protein systems, including the protein capsid of TBSV with 488,000 atoms. The computational times for NEIMO and CMM are demonstrated to scale linearly with size. With NEIMO the dynamics time steps can be as large as 20 fs (for small peptides), much larger than possible with standard Cartesian coordinate dynamics.For TBSV we considered both the normal form and the high pH form, in which the Ca2+ ions are removed. These calculations lead to a contraction of the protein for both forms (probably because of ignoring the RNA core not observed in the X-ray). © 1994 Wiley-Liss, Inc.
    Additional Material: 21 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200304
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    Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 68-84 
    Details
    ISSN: 0887-3585
    Keywords: side chain conformation ; protein folding ; protein binding ; helix formation ; helix stability ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Theoretical estimations of changes in side chain configurational entropy are essential for understanding the different contributions to the overall thermodynamic behavior of important biological processes like folding and binding. The configurational entropy of any given side chain in any particular protein can be evaluated from the complete energy profile of the side chain. Calculations of the energy profiles can be performed using the side chain single bond dihedrals as the only independent variables as long as the structures at each value of the dihedrals are allowed to relax through small changes in the valence bond angles. The probabilities of different side chain conformers obtained from these energy profiles are very similar to the conformer populations obtained by analysis of side chain preferences in the proteins of the Protein Data Bank. Also, side chain conformational entropies obtained from the energy profiles agree extremely well with those obtained from the Protein Data Bank conformer populations. Changes in side chain configurational entropy in binding and folding can be computed as differences in conformational entropy because, in most cases, the frequency of the rotational oscillation around the energy minimum of any given conformer does not appear to change significantly in the reaction. Changes of side chain conformational entropy calculated in this way were compared with experimental values. The only available experimental data-the effect of side chain substitution on the stability of α-helices-were used for this comparison. The experimental values were corrected to subtract the solvent contributions. This comparison yields an excellent agreement between calculated and experimental values, validating not only the theoretical estimates but also the separability of the entropic contributions into configurational terms and solvation related terms. © 1994 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200108
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    Microtube batch protein crystallization: Applications to human immunodeficiency virus type 2 (HIV-2) protease and human renin (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 98-102 
    Details
    ISSN: 0887-3585
    Keywords: X-ray diffraction ; aspartic protease ; AIDS ; recombinant protein ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: For therapeutically relevant targets, the evaluation of enzymes in complex with their inhibitors by cocrystallization and high resolution structural analysis has become a vital component of structure-driven drug design and development. Two approaches, hanging drop vapor diffusion and a novel microtube batch method, were utilized in parallel to grow crystals of recombinant HIV -2 protease and recombinant human renin in complex with inhibitors. In the case of HIV -2 protease in complex with a reduced amide inhibitor, crystallization was achieved only by the microbatch method. In the case of human renin, the addition of precipitant was required for crystal growth. The microbatch method described here is a useful supplementary or alternative approach for screening parameters and generating crystals suitable for high resolution structural analysis. © 1994 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200110
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    Solvent-induced organization: A physical model of folding myoglobin (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 124-138 
    Details
    ISSN: 0887-3585
    Keywords: leghemoglobin ; hydrophobic ; interactions ; hydrophobicity ; protein folding ; structure prediction ; protein dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The essential features of the in vitro refolding of myoglobin are expressed in a solvable physical model. Alpha helices are taken as the fundamental collective coordinates of the system, while the refolding is assumed to be mainly driven by solvent-induced hydrophobic forces. A quantitative model of these forces is developed and compared with experimental and theoretical results. The model is then tested by being employed in a simulation scheme designed to mimic solvent effects. Realistic dynamic trajectories of myoglobin are shown as it folds from an extended conformation to a close approximation of the native state. Various suggestive features of the process are discussed. The tenets of the model are further tested by folding the single-chain plant protein leghemoglobin. © 1994 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200203
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    An evaluation of implicit and explicit solvent model systems for the molecular dynamics simulation of bacteriophage T4 lysozyme (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 19-33 
    Details
    ISSN: 0887-3585
    Keywords: Discover program ; protein dynamics ; computer simulation ; protein motions ; counterions ; dielectric ; protein electrostatics ; aqueous simulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In this report we examine several solvent models for use in molecular dynamics simulations of protein molecules with the Discover program from Biosym Technologies. Our goal was to find a solvent system which strikes a reasonable balance among theoretical rigor, computational efficiency, and experimental reality. We chose phage T4 lysozyme as our model protein and analyzed 14 simulations using different solvent models. We tested both implicit and explicit solvent models using either a linear distance-dependent dielectric or a constant dielectric. Use of a linear distance-dependent dielectric with implicit solvent significantly diminished atomic fluctuations in the protein and kept the protein close to the starting crystal structure. In systems using a constant dielectric and explicit solvent, atomic fluctuations were much greater and the protein was able to sample a larger portion of conformational space. A series of nonbonded cutoff distances (9.0, 11.5, 15.0, 20.0 Å) using both abrupt and smooth truncation of the nonbonded cutoff distances were tested. The method of dual cutoffs was also tested. We found that a minimum nonbonded cutoff distance of 15.0 Å was needed in order to properly couple solvent and solute. Distances shorter than 15.0 Å resulted in a significant temperature gradient between the solvent and solute. In all trajectories using the proprietary Discover switching function, we found significant denaturation in the protein backbone; we were able to run successful trajectories only in those simulations that used no switching function. We were able to significantly reduce the computational burden by using dual cutoffs and still calculate a quality trajectory. In this method, we found that an outer cutoff distance of 15.0 Å and an inner cutoff distance of 11.5 worked well. While a 10 Å shell of explicit water yielded the best results, a 6 A shell of water yielded satisfactory results with nearly a 40% reduction in computational cost. © 1994 John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180105
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    Molecular surface representations by sparse critical points (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 94-101 
    Details
    ISSN: 0887-3585
    Keywords: surface representation ; molecular recognition ; protein docking ; surface triangulation ; molecular graphics ; molecular visualization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have defined a molecular surface representation that describes precisely and concisely the complete molecular surface. The representation consists of a limited number of critical points disposed at key locations over the surface. These points adequately represent the shape and the important characteristics of the surface, despite the fact that they are modest in number. We expect the representation to be useful in areas such as molecular recognition and visualization. In particular, using this representation, we are able to achieve accurate and efficient protein-protein and protein-small molecule docking. © 1994 John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180111
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  • 84
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    Lobster enolase crystallized by serendipity (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 390-393 
    Details
    ISSN: 0887-3585
    Keywords: protein crystallization ; enzyme copurification ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An unknown protein crystallized from a lobster muscle preparation in which arginine kinase was the majority component. It was identified as enolase by peptide sequencing and activity testing, and a SIRAS electron density map showed its three-dimensional structure to be very similar to that of yeast enolase. © 1994 John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180409
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    Crystallographic analysis of oxygenated and deoxygenated states of arthropod hemocyanin shows unusual differences (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 302-309 
    Details
    ISSN: 0887-3585
    Keywords: dinuclear copper site ; hemocyanin ; oxygen binding ; allosteric regulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The X-ray structure of an oxygenated hemocyanin molecule, subunit II of Limulus polyphemus hemocyanin, was determined at 2.4 Å resolution and refined to a crystallographic R-factor of 17.1%. The 73-kDa subunit crystallizes with the symmetry of the space group R32 with one subunit per asymmetric unit forming hexamers with 32 point group symmetry. Molecular oxygen is bound to a dinuclear copper center in the protein's second domain, symmetrically between and equidistant from the two copper atoms. The copper-copper distance in oxygenated Limulus hemocyanin is 3.6 ± 0.2 Å, which is surprisingly 1 Å less than that seen previously in deoxygenated Limulus polyphemus subunit II hemocyanin (Hazes et al., Protein Sci. 2:597, 1993). Away from the oxygen binding sites, the tertiary and quaternary structures of oxygenated and deoxygenated Limulus subunit II hemocyanins are quite similar. A major difference in tertiary structures is seen, however, when the Limulus structures are compared with deoxygenated Panulirus interruptus hemocyanin (Volbeda, A., Hol, W. G. J. J. Mol. Biol. 209:249, 1989) where the position of domain 1 is rotated by 8° with respect to domains 2 and 3. We postulate this rotation plays an important role in cooperativity and regulation of oxygen affinity in all arthropod hemocyanins. © 1994 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190405
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  • 86
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    Conservation and prediction of solvent accessibility in protein families (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 216-226 
    Details
    ISSN: 0887-3585
    Keywords: evolutionary information ; multiple alignments ; neural networks ; protein structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Currently, the prediction of three-dimensional (3D) protein structure from sequence alone is an exceedingly difficult task. As an intermediate step, a much simpler task has been pursued extensively: predicting 1D strings of secondary structure. Here, we present an analysis of another 1D projection from 3D structure: the relative solvent accessibility of each residue. We show that solvent accessibility is less conserved in 3D homologues than is secondary structure, and hence is predicted less accurately from automatic homology modeling; the correlation coefficient of relative solvent accessibility between 3D homologues is only 0.77, and the average accuracy of predictions based on sequence alignments is only 0.68. The latter number provides an effective upper limit on the accuracy of predicting accessibility from sequence when homology modeling is not possible. We introduce a neural network system that predicts relative solvent accessibility (projected onto ten discrete states) using evolutionary profiles of amino acid substitutions derived from multiple sequence alignments. Evaluated in a cross-validation test on 238 unique proteins, the correlation between predicted and observed relative accessibility is 0.54. Interpreted in terms of a three-state (buried, intermediate, exposed) description of relative accessibility, the fraction of correctly predicted residue states is about 58%. In absolute terms this accuracy appears poor, but given the relatively low conservation of accessibility in 3D families, the network system is not far from its likely optimal performance. The most reliably predicted fraction of the residues (50%) is predicted as accurately as by automatic homology modeling. Prediction is best for buried residues, e.g., 86% of the completely buried sites are correctly predicted as having 0% relative accessibility. © 1994 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200303
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    Molecular dynamics simulations of trp apo-and holorepressors: Domain structure and ligand-protein interaction (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 248-258 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; trp-repressor ; ligand ; domain ; dynamic cross-correlation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics simulations of the apo- and holo-forms of thetrp-repressor protein were performed under extensively solvated conditions in order to elucidate their dynamic structures and ligand-protein interactions. The root mean square fluctuations calculated from the trajectories agreed with those calculated from X-ray temperature factors. Distance, distance fluctuation, and dynamic cross-correlation maps were drawn to provide information on the dynamic structures and communications among the domains. A three-domain format has been proposed for the crystal structure (Zhang et at., Nature 327:591-597, 1987) namely, helices A-C and F of both subunits make up a central core, and D and E of each subunit forms a DNA binding head. The results of the simulations were mostly consistent with the three-domain format. However, helix F was more flexible and freer than other parts of the central core. The turn DE, the helix-turn-helix DNA binding motif, was free from interactions and correlations with other domains in both forms of the repressor. A comparison of the simulations of the aporepressor and holorepressor showed that tryptophan binding made the DNA-binding helix D more flexible but helix F less flexible. Several amino acid residues in contact with the bound tryptophan were identified as making concerted motions with it. Interaction energies between the corepressor and the amino acid residues of the protein were analyzed; the results were mostly consistent with the mutational experiments. © 1994 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200305
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    Magnetic resonance studies of the binding of oligonucleotide substrates to mutants of staphylococcal nuclease (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 68-80 
    Details
    ISSN: 0887-3585
    Keywords: staphylococcal nuclease ; nonproductive substrate binding to ; subsites of ; active site mutants of ; oligonucleotide binding to ; Ca2+ binding to ; Mn2+ binding to ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: By a combination of NMR docking and model building, the substrate binding site on staphylococcal nuclease was found to accommodate a trinucleotide and to consist of three subsites, each interacting with a single nucleotidyl unit of DNA. Binding of the essential Ca2+ activator and substrate cleavage occur between subsites 1 and 2. Hence, catalytically productive binding would span subsites 1 and 2 while nonproductive binding would span subsites 2 and 3. Lys-49 is near subsite 1, and Lys-84 and Tyr-115 interact with substrates at sub site 3 [Weber, D. J., Gittis, A. G., Mullen, G. P., Abeygunawardana, C., Lattman, E. E., Mildvan, A. S. Proteins 13:275-287, 1992]. The proposed locations of these subsites were independently tested by the effects of the K49A, K84A, and Y115A mutations of staphylococcal nuclease on the binding of Mn2+, Ca2+, and the dinucleotide and trinucleotide substrates, 5′-pdTdA, dTdA, and dTdAdG. These three mutants have previously been shown to be fully active and to have CD and 2D NMR spectra very similar to those of the wild-type enzyme (Chuang, W.-J., Weber, D. J., Gittis, A. G., Mildvan, A. S. Proteins 17:36-48, 1993). All three mutant enzymes and their pdTdA and dTdA complexes (but not their dTdAdG complex) bind Mn2+ and Ca2+ more weakly than the wild-type enzyme by factors ranging from 2 to 11. The presence of a terminal phosphate as in 5′-pdTdA raises the affinity of the substrate for staphylococcal nuclease and its three mutants by two orders of magnitude and for the corresponding enzyme-metal complexes by three to four orders of magnitude, suggesting that the terminal phosphate is coordinated by the enzyme-bound divalent cation. Such complexation would result in the nonproductive binding of 5′-pdTdA at subsites 2 and 3. Accordingly, the K84A and Y115A mutations significantly weaken the binding of 5′-pdTdA and its metal to staphylococcal nuclease by factors of 2.2 to 37.8, while the K49A mutation has much smaller or no effect. Such nonproductive binding explains the low activity of staphylococcal nuclease with small substrates, especially those With a terminal phosphate. Similarly, the K84A and Y115A mutations weaken the binding of dTdA and its metal complexes to the enzyme by factors of 3.4 to 13.1 while the K49A mutation has smaller effects indicating significant nonproductive binding of dTdA. The trinucleotide dTdAdG binds more tightly to wild-type and mutant staphylococcal nuclease and to its metal complexes than does the dinucleotide dTdA by factors of 2.4 to 12.2, reflecting the occupancy of an additional subsite. Predominantly productive binding of dTdAdG is indicated by the 1.7- to 8.3-fold lower affinities of the K49A, K84A, and Y115A mutants for the trinucleotide and its metal complexes. The largest effects on dTdAdG binding are seen with the Y115A mutation presumably reflecting the dual role of Tyr-115 both in donating a hydrogen bond to a phosphodiester oxygen between subsites 2 and 3 and in stacking onto the guanine base at subsite 3. © 1994 John Wiley & Sons, Inc.
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    New Developments at PROTEINS (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180102
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    Rigid-body docking with mutant constraints of influenza hemagglutinin with antibody HC19 (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 8-18 
    Details
    ISSN: 0887-3585
    Keywords: docking algorithm ; antigen-antibody complex ; epitope ; influenza virus hemagglutinin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An automatic docking algorithm has been applied to the modeling of the complex between hemagglutinin from influenza virus and the Fab fragment of a monoclonal antibody raised against this antigen. We have introduced here the use of biochemical information provided by mutants of hemagglutinin. The docking procedure finds a small number of candidate solutions where three sites of escape mutations are buried and form hydrogen bonds in the interface. The localization of the epitope is improved by additional biochemical data about mutants that do not affect antibody binding. Five candidate solutions with low energy, reasonably well-packed interfaces, and six to ten hydrogen bonds are compatible with mutant information. One of the five stands out as generally better than the others from these points of views. © 1994 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340180104
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  • 91
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    Alpha helix capping in synthetic model peptides by reciprocal side chain-main chain interactions: Evidence for an N terminal “capping box” (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 1-7 
    Details
    ISSN: 0887-3585
    Keywords: α-helix capping ; α-helix initiation ; α-helix termination ; synthetic peptides ; protein folding ; circular dichroism ; 1H nmr ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A significant fraction of the amino acids in proteins are alpha helical in conformation. Alpha helices in globular proteins are short, with an average length of about twelve residues, so that residues at the ends of helices make up an important fraction of all helical residues. In the middle of a helix, H-bonds connect the NH and CO groups of each residue to partners four residues along the chain. At the ends of a helix, the H-bond potential of the main chain remains unfulfilled, and helix capping interactions involving bonds from polar side chains to the NH or CO of the backbone have been proposed and detected. In a study of synthetic helical peptides, we have found that the sequence Ser-Glu-Asp-Glu stabilizes the alpha helix in a series of helical peptides with consensus sequences. Following the report by Harper and Rose, which identifies SerXaaXaaGlu as a member of a class of common motifs at the N termini of alpha helices in proteins that they refer to as “capping boxes,” we have reexamined the side chain-main chain interactions in a varient sequence using 1H NMR, and find that the postulated reciprocal side chain-backbone bonding between the first Ser and last Glu side chains and their peptide NH partners can be resolved: Deletion of two residues N terminal to the Ser-Glu-Asp-Glu sequence in these peptides has no effect on the initiation of helical structure, as defined by two-dimensional (2D) NMR experiments on this variant. Thus the capping box sequence Ser-Glu-Asp-Glu inhibits N terminal fraying of the N terminus of alpha helix in these peptides, and shows the side chain-main chain interactions proposed by Harper and Rose. It thus acts as a helix initiating signal. Since normal a helix cannot propagate beyond the N terminus of this structure, the box acts as a termination signal in this direction as well. © 1994 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180103
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  • 92
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    Cold adaption of enzymes: Structural comparison between salmon and bovine trypsins (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 149-166 
    Details
    ISSN: 0887-3585
    Keywords: crystal structure ; cold adaption ; catalytic efficiency ; protein stability ; anionic ; ectotherm ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of an anionic form of salmon trypsin has been determined at 1.82 Å resolution. We report the first structure of a trypsin from a phoikilothermic organism in a detailed comparison to mammalian trypsins in order to look for structural rationalizations for the cold-adaption features of salmon trypsin. This form of salmon trypsin (T II) comprises 222 residues, and is homologous to bovine trypsin (BT) in about 65% of the primary structure. The tertiary structures are similar, with an overall displacement in main chain atomic positions between salmon trypsin and various crystal structures of bovine trypsin of about 0.8 Å. Intramolecular hydrogen bonds and hydrophobic interactions are compared and discussed in order to estimate possible differences in molecular flexibility which might explain the higher catalytic efficiency and lower thermostability of salmon trypsin compared to bovine trypsin. No overall differences in intramolecular interactions are detected between the two structures, but there are differences in certain regions of the structures which may explain some of the observed differences in physical properties. The distribution of charged residues is different in the two trypsins, and the impact this might have on substrate affinity has been discussed. © 1994 Wiley-Liss, Inc.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340200205
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  • 93
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    Electronic Resource
    Collective motions in proteins investigated by X-ray diffuse scattering (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 34-48 
    Details
    ISSN: 0887-3585
    Keywords: normal mode refinement ; correlation function ; intra- and intermolecular correlation ; higher order scattering ; human lysozyme ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have developed theoretical models for analysis of X-ray diffuse scattering from protein crystals. A series of models are proposed to be used for experimental data with different degrees of precision. First, we propose the normal mode model, where conformational dynamics of a protein is assumed to occur mostly in a limited conformational subspace spanned by a small number of low-frequency normal modes in the protein. When high precision data are available, variances and covariances of the normal mode variables can be determined from experimental data using this model. For experimental data with lower degrees of precision, we introduce a series of simpler models. These models express the covariance matrix using relatively simple empirical correlation functions by assuming the correlation between a pair of atoms to be isotropic. As an application of these simpler models, we calculate diffuse-scattering patterns from a human lysozyme crystal to examine how each adjustable parameter in the models affects general features of the resulting patterns. The results of the calculation are summarized as follows. (1) The higher order scattering makes a significant contribution at high resolutions. (2) The resulting simulated patterns are sensitive to changes in correlation lengths of about 1 Å, as well as to changes of the functional form of the correlation function. (3) But only the “average” value of the intra- and intermolecular correlation lengths seems to determine the gross features of the pattern. (4) The effect of the atom-dependent amplitude of fluctuations is difficult to observe. © 1994 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180106
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  • 94
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    Electronic Resource
    The enzymatic mechanism of carboxypeptidase: A molecular dynamics study (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 186-197 
    Details
    ISSN: 0887-3585
    Keywords: carboxypeptidas ; molecular dynamics ; enzymatic mechanisms ; peptidase mechanism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An MD simulation of the system carboxypeptidase A (CPA) with the tetrapeptide Val-Leu-Phe-Phe has been performed in order to learn about the substrate disposition just prior to nucleophilic attack. We have explored the model in which the substrate does not substitute the zinc-coordinated water (the “water” mechanism). The simulations do suggest as feasible that the Zn-OH2 group performs a nucleophilic attack on the Phe-Phe peptidic bond. We have also investigated the model in which the carbonyl oxygen displaces the zinc-coordinated water. In this case the substrate and Glu-270 orient themselves to allow an anhydride intermediate during the peptidic bond cleavage (the “anhydride” mechanism). Based on the results of the simulations, both “water” and “anhydride” mechanisms are structurally feasible, although the former model seems more probable on chemical grounds. © 1994 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180210
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  • 95
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    Electronic Resource
    A molecular dynamics approach for the generation of complete protein structures from limited coordinate data (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 174-185 
    Details
    ISSN: 0887-3585
    Keywords: computer modeling ; protein structure prediction ; α-carbons ; structure evaluation ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Generation of full protein coordinates from limited information, e.g., the Cα coordinates, is an important step in protein homology modeling and structure determination, and molecular dynamics (MD) simulations may prove to be important in this task. We describe a new method, in which the protein backbone is built quickly in a rather crude way and then refined by minimization techniques. Subsequently, the side chains are positioned using extensive MD calculations. The method is tested on two proteins, and results compared to proteins constructed using two other MD-based methods. In the first method, we supplemented an existing backbone building method with a new procedure to add side chains. The second one largely consists of available methodology. The constructed proteins are compared to the corresponding X-ray structures, which became available during this study, and they are in good agreement (backbone RMS values of 0.5-0.7 Å, and all-atom RMS values of 1.5-1.9 Å). This comparative study indicates that extensive MD simulations are able, to some extent, to generate details of the native protein structure, and may contribute to the development of a standardized methodology to predict reliably (parts of) protein structures when only partial coordinate data are available. © 1994 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180209
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  • 96
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    Electronic Resource
    Introducing “Future Directions” (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180202
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  • 97
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    Electronic Resource
    Crystallization and characterization of colicin E1 channel-forming polypeptides (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 150-157 
    Details
    ISSN: 0887-3585
    Keywords: X-ray crystallography ; membrane protein ; ion channels ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of the channel-forming domain of colicin E1 from E. coli were grown by vapor diffusion at pH 6.4 and higher pH values. Cleavage of the colicin molecule with trypsin or thermolysin produced two of the pore-forming polypeptides used in these experiments. The third polypeptide was purified from a constructed plasmid that overexpresses only the C-terminal domain of colicin E1. Polypeptide crystals are tetragonal with space group I4, have one monomer in the asymmetric unit, and diffract to 2.2-2.4 Å. Unit cell parameters for the tryptic and thermolytic polypeptides are a = 102.9 Å and c = 35.6 Å. Crystals of the overexpressed polypeptide have unit cell parameters of a =87.2 Å and c =59.1 Å. The crystals were characterized by precession photography, and native data sets of each channel-forming fragment were collected on a Siemens-Nicolet area detector. The crystallization and characterization of these polypeptides are the first steps in the structure determination of the channel-forming domain of colicin E1. © 1994 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190208
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  • 98
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    Electronic Resource
    A model for the structure of a homodimeric prohormone: The precursor to the locust neuropeptide AKH I (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 356-366 
    Details
    ISSN: 0887-3585
    Keywords: NMR ; structure determination ; coiled coil ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have determined the structure in solution of a homodimeric protein that is a precursor to the locust neuropeptide adipokinetic hormone I using nuclear magnetic resonance spectroscopy. This precursor, called P1, is comprised of two 41 residue strands joined by a single inter-chain disulphide at Cys39. We have also determined the structure of an end product of P1 processing, called APRP1; this is a homodimer comprised of residues 14-41 of PI. Nuclear Overhauser Effect (nOe) data indicate that in both P1 and APRP1, residues 22-37 (numbered with respect to P1) form pairs of α-helices, with no evidence for any other secondary structure. © 1994 Wiley-Liss, Inc.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340200408
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  • 99
    Electronic Resource
    Electronic Resource
    Molecular dynamics simulation of the docking of substrates to proteins (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 174-182 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; docking ; computer simulation ; substrate docking ; immunoglobulin ; rational drug design ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A simple method is described to perform docking of subtrates to proteins or probes to receptor molecules by a modification of molecular dynamics simulations. The method consists of a separation of the center-of-mass motion of the substrate from its internal and rotational motions, and a separate coupling to different thermal baths for both types of motion of the substrate and for the motion of the receptor. Thus the temperatures and the time constants of coupling to the baths can be arbitrarily varied for these three types of motion, allowing either a frozen or a flexible receptor and allowing control of search rate without disturbance of internal structure. In addition, an extra repulsive term between substrate and protein was applied to smooth the interaction. The method was applied to a model substrate docking onto a model surface, and to the docking of phosphocholine onto immunoglobulin McPC603, in both cases with a frozen receptor. Using transrational temperatures of the substrate in the range of 1300-1700 K and room temperature for the internal degrees of freedom of the substrate, an efficient nontrapping exploratory search (“helicopter view”) is obtained, which visits the correct binding sites. Low energy conformations can then be further investigated by separate search or by dynamic simulated annealing. In both cases the correct minima were identified. The possibility to work with flexible receptors is discussed. © 1994 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190303
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  • 100
    Electronic Resource
    Electronic Resource
    Spatial optimization of electrostatic interactions between the ionized groups in globular proteins (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 222-229 
    Details
    ISSN: 0887-3585
    Keywords: protein electrostatics ; energy calculations ; ion pairs ; Monte-Carlo simulations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A model approach is suggested to estimate the degree of spatial optimization of the electrostatic interactions in protein molecules. The method is tested on a set of 44 globular proteins, representative of the available crystallographic data. The theoretical model is based on macroscopic computation of the contribution of charge-charge interactions to the electrostatic term of the free energy for the native proteins and for a big number of virtual structures with randomly distributed on protein surface charge consetellations (generated by a Monte-Carlo technique). The statistical probability of occurrence of random structures with electrostatic energies lower than the energy of the native protein is suggested as a criterion for spatial optimization of the electrostatic interactions. The results support the hypothesis that the folding process optimizes the stabilizing effect of electrostatic interactions, but to very different degree for different proteins. A parallel analysis of ion pairs shows that the optimization of the electrostatic term in globular proteins has increasingly gone in the direction of rejecting the repulsive short contacts between charges of equal sign than of creating of more salt bridges (in comparison with the statistically expected number of shortrange ion pairs in the simulated random structures). It is observed that the decrease in the spatial optimization of the electrostatic interactions is usually compensated for by an appearance of disulfide bridges in the covalent structure of the examined proteins. © 1994 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190306
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