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  • 1
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Biochemistry 21 (1982), S. 5329-5334 
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 38 (1994), S. 583-592 
    ISSN: 1432-1432
    Keywords: Silk fibroin gene ; Unequal crossover ; Three-tiered higher-order structure ; Codon usage ; Repetitive sequence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have sequenced a number of cDNAs representing the Bombyx mori silk fibroin heavy chain transcript. These reveal that the central region of the fibroin gene is composed of alternate arrays of the crystalline element a and the noncrystalline element b. The core region is partitioned by a homogeneous nonrepetitive amorphous domain of around 100 by in length. The element a is characterized by repeats of a highly conserved 18-bp sequence coding for perfect repeats of the unit peptide Gly-Ala-Gly-Ala-Gly-Ser. The element b is composed of repeats of a less-conserved 30-bp sequence which codes for a peptide similar to that in element a except in that (1) Ser is replaced by Tyr and (2) there are irregular substitutions of Ala to Val or Tyr. Therefore, the structure of the fibroin gene core consists of three-step higher-order periodicities. Heterogeneities in numbers of repeats are observed in each step of periodicity. Boundary sequence appeared in each periodicity to be quite homogeneous. Sequence analysis indicates that the unit sequences of elements a and b have homology to those of recombination hotspots reported in other genes and a recombination event may frequently occur between the misaligned sister chromatids, resulting in heterogeneities in repeat numbers and duplication or deletion of repetitive sequences. The repetitive superstructure of the fibroin gene may have been a result of continuous unequal crossovers in a primordial gene during evolution. A couple of important features of the fibroin protein were proved by the present nucleotide sequencing. The amino acid representation of the amorphous domain is vastly different from that of the repetitive regions. The carboxy-terminal nonrepetitive region has three Cys and nine (Arg + Lys) residues that may be responsible for complex formation with the fibroin light-chain molecule. The present DNA analysis also clearly demonstrates that the tRNA population in the posterior silk gland strictly complements the frequency of codons in the fibroin mRNA, which may help to achieve a highly efficient translation of fibroin mRNA.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 45 (1997), S. 253-264 
    ISSN: 1432-1432
    Keywords: Key words: Retrotransposon — LINE — Non-LTR retrotransposon —Bombyx mori, Insect — Histone genes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Repetitive sequences with oligo A tails were observed in Dra1 fragments of Bombyx mori genomic DNA. The full sequence of the element, an abundant non-LTR retrotransposon of B. mori, was determined by assembling inner restriction fragments. This element, designated L1Bm, contained two ORFs encoding a gag-like protein and reverse transcriptase (RT), respectively. An endonuclease domain was identified at the N-terminus of the RT sequence. The homology search of the amino acid sequences revealed that L1Bm belongs evolutionally to the same family as various other non-LTR retrotransposons of Drosophila and Mosquito. On the other hand, L1Bm resembles the L1 element of human genome in its high copy number and its frequent truncation at the 5′-side. Some units of the histone gene repeat in B. mori possess complete L1Bm elements in a 3′-flanking region of H2b.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 51 (2000), S. 161-165 
    ISSN: 1432-1432
    Keywords: Key words: Polyubiquitin gene — Orthologue — Synonymous substitution — Synonymous sequence difference — Concerted evolution — Phylogenetic tree
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The polyubiquitin gene, encoding tandemly repeated multiple ubiquitins, constitutes a uniquitin gene subfamily. It has been demonstrated that polyubiquitin genes are subject to concerted evolution; namely, the individual ubiquitin coding units contained within a polyubiquitin gene are more similar to one another than they are to the ubiquitin coding units in the orthologous gene from other species. However there has been no comprehensive study on the concerted evolution of polyubiquitin genes in a wide range of species, because the relationships (orthologous or paralogous) among multiple polyubiquitin genes from different species have not been extensively analyzed yet. In this report, we present the results of analyzing the nucleotide sequence of polyubiquitin genes of mammals, available in the DDBJ/EMBL/GenBank nucleotide sequence databases, in which we found that there are two groups of polyubiquitin genes in an orthologous relationship. Based on this result, we analyzed the concerted evolution of the polyubiquitin gene in various species and compared the frequency of concerted evolutionary events interspecifically by taking into consideration that the rate of synonymous substitution at the polyubiquitin gene locus may vary depending on species. We found that the concerted evolutionary events in polyubiquitin genes have been more frequent in rats and Chinese hamsters than those in humans, cows, and sheep. The guinea pig polyubiquitin gene was an intermediate example. The frequency of concerted evolution in the mouse gene was unexpectedly low compared to that of other rodent genes.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 33 (1991), S. 216-225 
    ISSN: 1432-1432
    Keywords: Ubiquitin gene ; Codon usage ; Molecular evolution ; Gene organization ; Sequence comparison
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Ubiquitin is ubiquitous in all eukaryotes and its amino acid sequence shows extreme conservation. Ubiquitin genes comprise direct repeats of the ubiquitin coding unit with no spacers. The nucleotide sequences coding for 13 ubiquitin genes from 11 species reported so far have been compiled and analyzed. The G+C content of codon third base reveals a positive linear correlation with the genome G+C content of the corresponding species. The slope strongly suggests that the overall G+C content of codons of polyubiquitin genes clearly reflects the genome G+C content by AT/GC substitutions at the codon third position. The G+C content of ubiquitin codon third base also shows a positive linear correlation with the overall G+C content of coding regions of compiled genes, indicating the codon choices among synonymous codons reflect the average codon usage pattern of corresponding species. On the other hand, the monoubiquitin gene, which is different from the polyubiquitin gene in gene organization, gene expression, and function of the encoding protein, shows a different codon usage pattern compared with that of the polyubiquitin gene. From comparisons of the levels of synonymous substitutions among ubiquitin repeats and the homology of the amino acid sequence of the tail of monomeric ubiquitin genes, we propose that the molecular evolution of ubiquitin genes occurred as follows: Plural primitive ubiquitin sequences were dispersed on genome in ancestral eukaryotes. Some of them situated in a particular environment fused with the tail sequence to produce monomeric ubiquitin genes that were maintained across species. After divergence of species, polyubiquitin genes were formed by duplication of the other primitive ubiquitin sequences on different chromosomes. Differences in the environments in which ubiquitin genes are embedded reflect the differences in codon choice and in gene expression pattern between poly- and monomeric ubiquitin genes.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 35 (1992), S. 123-130 
    ISSN: 1432-1432
    Keywords: Genomic evolution ; Repetitive sequences ; Duplication of DNA sequences ; Bombyx mori ; Silk fibroin gene
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The Bombyx fibroin gene has a discrete mosaic structure of various repetitive sequences, which may have evolved through various repeating arrangements. Detailed sequence analysis of the fibroin gene containing coding and noncoding regions revealed that the whole sequence could be arranged as an array of short repetitive sequences. A portion of the intron of the fibroin gene is one of interspersed repetitive elements. We cloned a 1.5-kb DNA fragment of the Bombyx genome that contains interspersed elements homologous to the intron sequence. Sequence comparison between the intron and the 1.5-kb fragment shows that partial duplication has frequently occurred in evolutionary progress, and the resultant repetitive blocks of short motif sequences are abundant in the genome. These facts suggest that tandem duplication of the short motif sequence is an important rearrangement in genomic evolution of the fibroin gene.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 79 (1975), S. 2108-2112 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1432-1777
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract. We previously obtained a monoclonal antibody (Th-10a mAb) that recognizes a single 95-kDa mouse nuclear protein (NP95). Immunostaining analyses revealed that the NP95 was specifically stained in the S phase of normal mouse thymocytes. In contrast, mouse T cell lymphoma cells exhibited a constantly high level of NP95 accumulation irrespective of cell stages during the cell cycle. In the present study, we isolated the cDNA encoding the NP95 from a λgt-11 cDNA expression library, using the Th-10a mAb. Sequencing of the whole 3.5-kb cDNA revealed that NP95 is a novel nuclear protein with an open reading frame (ORF) consisting of 782 amino acids. The ORF contains a zinc finger motif, a potential ATP/GTP binding site, a putative cyclin A/E-cdk2 phosphorylation site, and the retinoblastoma protein (RB)-binding motif ``IXCXE''. The chromosomal location of Np95 gene was determined by fluorescence in situ hybridization. Np95 gene locates on mouse Chromosome (Chr) 17DE1.1. and rat Chr 9q11.2–q12.1. Np95 was strongly expressed in the testis, spleen, thymus, and lung tissues, but not in the brain, liver, or skeletal muscles. These results collectively implicate this novel nuclear protein in cell cycle progression and/or DNA replication.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 17 (1978), S. 2769-2782 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational transition of poly(L-agrignine) by binding with various mono-, di-, and polyvalent anions, especially with SO2-4, was studied by CD measurements. The intramolecular random coil-to-α-helix conformational transition and the subsequent transition to the β-turn-like structure was caused by binding with SO2-4. The binding data obtained from equilibrium dialysis experiments showed that the α-helical conformation of poly(L-arginine) is stabilized at a 1:3 stoichiometric ratio of bound SO2-4 to arginine residue; at higher free SO2-4 concentrations, the α-helix converts to the β-turn-like structure accompanied by a decrease in amount of bound SO2-4. The same conformaitonal transition of poly(L-arginine) also occurred in the solutions of other divalent anions (SO2-4, CO2-3, and HPO2-4) and polyvalent anions (P2O4-7, P3O5-10). Among the monovalent anions examined, CIO-4 and dodecyl sulfate were effective in including α-helical conformation, while the other monovalent anions (OH-, Cl-, F-, H2PO-4, HCO-3 and CIO-3) failed to induce poly(L-arginine) to assume the α-helical conformation. Thus, we noticed that, except for dodecyl sufate, the terahedral structure is common to the α-helix-forming anions. A well-defined model to the α-helical poly(L-arginine)/anion complex was proposed, in which both the binding stoichiometry of anions to the arginine residue and the tetrahedral structure of anions were taken into consideration. Based on these results, it was concluded that the tetrahedral-type anions stabilize the α-helical conformation of poly(L-arginine) by crosslinking between two guanidinium groups of nearby side chains on the same α-helix through the ringed structures stabilized by hydrogen bonds as well as by electrostatic interaction. Throughout the study it was noticed that the structural behavior of poly(L-arginine) toward anions is distinct from that of poly(L-lysine).
    Additional Material: 13 Ill.
    Type of Medium: Electronic Resource
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