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41.
Stephen F. Altschul 《Journal of molecular evolution》1993,36(3):290-300
Summary Protein sequence alignments generally are constructed with the aid of a substitution matrix that specifies a score for aligning each pair of amino acids. Assuming a simple random protein model, it can be shown that any such matrix, when used for evaluating variable-length local alignments, is implicitly a log-odds matrix, with a specific probability distribution for amino acid pairs to which it is uniquely tailored. Given a model of protein evolution from which such distributions may be derived, a substitution matrix adapted to detecting relationships at any chosen evolutionary distance can be constructed. Because in a database search it generally is not known a priori what evolutionary distances will characterize the similarities found, it is necessary to employ an appropriate range of matrices in order not to overlook potential homologies. This paper formalizes this concept by defining a scoring system that is sensitive at all detectable evolutionary distances. The statistical behavior of this scoring system is analyzed, and it is shown that for a typical protein database search, estimating the originally unknown evolutionary distance appropriate to each alignment costs slightly over two bits of information, or somewhat less than a factor of five in statistical significance. A much greater cost may be incurred, however, if only a single substitution matrix, corresponding to the wrong evolutionary distance, is employed. 相似文献
42.
T. Jermy 《Entomologia Experimentalis et Applicata》1993,66(1):3-12
Most hypotheses concerning the evolution of insect-plant relationships are based on the assumptions that, (1) phytophagous
insects reduce plant fitness, and that (2) insect-plant relationships are the result of unconstrained selection. It can be
shown, however, that there is little evidence to support these assumptions. As an alternative, it is proposed that the evolution
of insect-plant relationships results primarily from autonomous evolutionary events; namely from heritable functional changes
within the insects' nervous system that determine plant recognition and ultimately host plant specificity. These changes cannot
be evoked by selective ecological agents. They originate from intrinsic changes (mutationssensu lato) within the insect genome. Ecological factors play a secondary role: by either supporting or preventing the establishment
of the new genotype with the novel food preference.
This paper has been dedicated in warm friendship to Professor Louis M. Schoonhoven, the leading scientist in sensory physiology
of phytophagous insects, on the occasion of his 60th birthday. 相似文献
43.
44.
This work studies the structure-function relationships of Asn135, a residue situated in the GTP binding pocket of elongation factor Tu (EF-Tu). For this purpose we constructed EF-TuN135D/D138N and assayed its reactivity towards various purine nucleotides. We found that EF-TuN135D/D138N had no functional effect with GTP, ATP, XTP and isoGTP. The lack of a productive interaction with isoGTP shows that the Asn135 side-chain does not recognize the exocyclic keto group of the guanine base. However, EF-TuN 135D/D 138N, whose native conformation is stabilized by either elongation factor Ts or kirromycin, was able to support the enzymatic binding of aa-tRNA to the ribosome in the absence of any nucleotide, when in complex with the antibiotic. Taken together, these results show that Asn135 is important for the correct folding of the nucleotide binding site and that EF-Tu·kirromycin can mediate the binding of aa-tRNA to the mRNA-programmed ribosomes independently of the native conformation of this site. 相似文献
45.
Summary We have improved zygote recovery 11–1,000 fold by optimizing the physiology of gamete release and mating inAcetabularia acetabulum. Gamete release was affected by agar purity, concentration, and volume/gametangial pair. Cold pre-treatment of gametangia (14–30 d at 10°C in the dark) synchronized subsequent gamete release at 21°C in the light. Cold pre-treatment was nearly twice as effective in synchronizing subsequent gamete release when intact, gametangia-bearing caps rather than isolated gametangia were pretreated. Synchronizing gamete release doubled mating efficiency. In a wild-type laboratory strain ofA. acetabulum, there were 1,561±207 gametes/gametangium which had half-lives of 14.5 d in 0.1% seawater-agar. We recovered 48–93% of the expected numbers of zygotes from a mass mating of 8 to 1,226 gametangia and 11–128% of the expected numbers of zygotes from mating single gametangial pairs: the large range in the calculated mating efficiency may be attributable to the variation in the numbers of gametes made per gametangium. Zygote recovery from single gametangial pairs was highly dependent on the volume of mating matrix. In addition, most zygotes recovered were unattached to any other zygotes in the subsequent generation (> 95% single cells from matings of 1–500 gametangial pairs). Our improvements in mating conditions and zygote recovery (1) have facilitated cell manipulation and culture ofA. acetabulum in the laboratory; and (2) have made controlled crosses for selection and genetic analysis of mutants feasible. These advances have removed a major barrier to genetic analysis of development inAcetabularia.Abbreviations LB
Luria-Bertani bacteriological broth
- SE
standard error of the mean
- Tg
agar gelling temperatures
- DAPI
4,6-diamidino-2-phenylindole 相似文献
46.
The class I glutamine (Gln) tRNA synthetase interacts with the anticodon and acceptor stem of glutamine tRNA. RNA hairpin helices were designed to probe acceptor stem and anticodon stem-loop contacts. A seven-base pair RNA microhelix derived from the acceptor stem of tRNAGln was aminoacylated by Gln tRNA synthetase. Variants of the glutamine acceptor stem microhelix implicated the discriminator base as a major identity element for glutaminylation of the RNA helix. A second RNA microhelix representing the anticodon stem-loop competitively inhibited tRNAGln charging. However, the anticodon stem-loop microhelix did not enhance aminoacylation of the acceptor stem microhelix. Thus, transduction of the anticodon identity signal may require covalent continuity of the tRNA chain to trigger efficient aminoacylation. 相似文献
47.
48.
A Monte Carlo algorithm that searches for the optimal docking configuration of hen egg white lysozyme to an antibody is developed. Both the lysozyme and the antibody are kept rigid. Unlike the work of other authors, our algorithm does not attempt to explicitly maximize surface contact, but minimizes the energy computed using coarse-grained pair potentials. The final refinement of our best solutions using all-atom OPLS potentials (Jorgensen and Tirado-Rives8) consistently yields the native conformation as the preferred solution for three different antibodies. We find that the use of an exponential distance-dependent dielectric function is an improvement over the more commonly used linear form. © 1993 Wiley-Liss, Inc. 相似文献
49.
Darja Fer
ej-Temeljotov Matev Kmet Darko Kocjan Sonja Kotnik Aleksander Resman Uro Urleb Katarina Verhnjak Igor Zver Janko
mitek 《Chirality》1993,5(4):288-292
Structure–interaction relationships, stereoselectivity, and solubility enhancement in inclusion compexation of β-cyclodextrins (CDs) with some racemic and enantiomerically pure 1,4-dihydropyridine derivatives (DHPs) were investigated. 1:1 and 1:2 (mole ratio) complexes were prepared and characterized by X-ray powder diffraction, differential scanning calorimetry (DSC), MS-FAB spectrometry, 1H-NMR spectroscopy, water and phase solubility. The solubility studies have revealed different complexation equilibria for optically pure DHP enantiomers, and corresponding racemic mixtures in water solutions. By means of 1H-NMR chemical shift measurements, the inclusion of aromatic fragments of racemic and enantiomerically pure DHP molecules within the cavities of different CDs was elucidated. Considerable stereoselectivity in complexation interactions was observed. The results indicate the potential use of cyclodextrins as chiral selectors for enantiomeric resolution of 1,4-DHP calcium antagonists. © 1993 Wiley-Liss, Inc. 相似文献
50.
Males of the planthopper Ribautodelphax imitanswere exposed to playbacks of either conspecific or heterospecific (R. imitantoides)female calls during their development from egg to adult, and thereafter these, as well as naive males,were offered a two- way choice between these calls. Males of all treatments approached the conspecific call significantly more often. However, males primed by the conspecific call chose the heterospecific call almost four times less often than did males primed by heterospecific calls or naive males, thus showing that the preference for conspecific calls can be partly learned. Males primed by heterospecific calls performed very similarly to completely naive males, suggesting that the signal recognition mechanism is much less sensitive to heterospecific calls than to conspecific calls. Males with experience of the conspecific female call tended to take more time to reach the call source in the trials than both other types of males. The evolutionary implications of these findings are discussed. 相似文献