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51.
Identification of consensus patterns in unaligned DNA sequences known to be functionally related 总被引:16,自引:0,他引:16
Hertz Gerald Z.; Hartzell George W. III; Stormo Gary D. 《Bioinformatics (Oxford, England)》1990,6(2):81-92
We have developed a method for identifying consensus patternsin a set of unaligned DNA sequences known to bind a common proteinor to have some other common biochemical function. The methodis based on a tnatrix representation of binding site patterns.Each row of the matrix represents one of the four possible bases,each column represents one of the positions of the binding siteand each element is determined by the frequency the indicatedbase occurs at the indicated position. The goal of the methodis to find the most significant matrix-i.e. the one with thelowest probability of occurring by chance-out of all the matricesthat can be formed from the set of related sequences. The reliabilityof the method improves with the number of sequences, while thetime required increases only linearly with the number of sequences.To test this method, we analysed 11 DNA sequences containingpromoters regulated by the Escherichia coli LexA protein. Thematrices we' found were consistent with the known consensussequence, and could distinguish the generally accepted LexAbinding sites from other DNA sequences.
Received on November 6, 1989; accepted on December 20, 1989 相似文献
52.
Desensitization of the Neurokinin 1 Receptor Is Mediated by the Receptor Carboxy-Terminal Region, but Is Not Caused by Receptor Internalization 总被引:1,自引:0,他引:1
Abstract: The carboxy-terminal cytoplasmic regions of the rat neurokinin 1 (substance P) and neurokinin 2 (neurokinin A) receptors have been exchanged to determine if this region of the neurokinin 1 receptor is involved in its desensitization. When expressed at similar levels in stably transfected Chinese hamster ovary (CHO) cell lines, receptors containing the carboxy-terminal region of the neurokinin 1 receptor desensitized significantly more (as measured by reduction of the inositol 1,4,5-trisphosphate response) when preexposed for 1 min to 1 µ M neurokinin, indicating a role for the carboxy-terminal region of the neurokinin 1 receptor in its desensitization. Measurement of receptor internalization using radiolabeled neurokinins (0.3 n M ) indicated that ∼75–80% of the receptors were internalized in each cell line after 10 min at 37°C, with no observable correlation between neurokinin receptor desensitization and internalization. Measurement of loss of receptor surface sites for cell lines CHO NK1 and CHO NK1NK2 following exposure to 1 µ M substance P also indicated no obvious relationship between the percent desensitization and percent of receptors internalized. Also, two inhibitors of neurokinin 1 receptor internalization, phenylarsine oxide and hyperosmolar sucrose, did not inhibit neurokinin 1 receptor desensitization. The protein kinase inhibitors Ro 31-8220, staurosporine, and Zn2+ had no effect on neurokinin 1 receptor desensitization, indicating that the kinases affected by these agents are not rate-limiting in neurokinin 1 receptor desensitization in this system. 相似文献
53.
Sulfonates: novel electron acceptors in anaerobic respiration 总被引:8,自引:0,他引:8
Thomas J. Lie Thomas Pitta E. R. Leadbetter Walter Godchaux III. Jared R. Leadbetter 《Archives of microbiology》1996,166(3):204-210
The enrichment and isolation in pure culture of a bacterium, identified as a strain of Desulfovibrio, able to release and reduce the sulfur of isethionate (2-hydroxyethanesulfonate) and other sulfonates to support anaerobic
respiratory growth, is described. The sulfonate moiety was the source of sulfur that served as the terminal electron acceptor,
while the carbon skeleton of isethionate functioned as an accessory electron donor for the reduction of sulfite. Cysteate
(alanine-3-sulfonate) and sulfoacetaldehyde (acetaldehyde-2-sulfonate) could also be used for anaerobic respiration, but many
other sulfonates could not. A survey of known sulfate-reducing bacteria revealed that some, but not all, strains tested could
utilize the sulfur of some sulfonates as terminal electron acceptor. Isethionate-grown cells of Desulfovibrio strain IC1 reduced sulfonate-sulfur in preference to that of sulfate; however, sulfate-grown cells reduced sulfate-sulfur
in preference to that of sulfonate.
Received: 2 May 1996 / Accepted: 8 June 1996 相似文献
54.
Edwin M. Everham III Randall W. Myster Eric VanDeGenachte 《American journal of botany》1996,83(8):1063-1068
Field experiments were conducted to investigate the effects of light, moisture, temperature, and litter on the regeneration of two early-, one mid-, and two late-successional tropical tree species. High light and litter seem to be universally good cues for regeneration, increasing seed/seedling survival for all species except for Cecropia (an early-successional species) whose small seeds may not be able to penetrate the litter layer. In addition, the high temperature environment in both artificially shaded and nonshaded areas of a natural gap exhibits less seed loss, an increase in the percent and rate of germination, and an increase in seedling survival for Dacryodes (a late-successional species), than the lower temperature environment under an intact canopy. Low soil water is also a good cue for Dacryodes germination as it is for Prestoea and Cecropia. Finally, the lower temperature environment found under the forest canopy (compared to the natural gap) leads to less seed loss and more germination for Guarea (a mid-successional species). Our results suggest that a good patch for regeneration of many species in this forest, early- as well as late-successional species, would have high light and a litter layer that moderates temperature and moisture extremes. The substantial variation in suitability among regeneration filters and species could: (1) contribute to low establishment success, i.e., most dispersed propagules do not become trees, (2) make it difficult to group species into germination strategies, and (3) make it hard to generalize about a net effect of any specific environmental variable on establishment. We suggest that tropical disturbances should be viewed in terms of their impact on a variety of environmental cues, which may signal germination and impact subsequent growth and survival. 相似文献
55.
56.
Abnormal bone growth and selective translational regulation in basic fibroblast growth factor (FGF-2) transgenic mice. 总被引:15,自引:2,他引:13
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J D Coffin R Z Florkiewicz J Neumann T Mort-Hopkins G W Dorn nd P Lightfoot R German P N Howles A Kier B A O'Toole et al. 《Molecular biology of the cell》1995,6(12):1861-1873
Basic fibroblast growth factor (FGF-2) is a pleiotropic growth factor detected in many different cells and tissues. Normally synthesized at low levels, FGF-2 is elevated in various pathologies, most notably in cancer and injury repair. To investigate the effects of elevated FGF-2, the human full-length cDNA was expressed in transgenic mice under control of a phosphoglycerate kinase promoter. Overexpression of FGF-2 caused a variety of skeletal malformations including shortening and flattening of long bones and moderate macrocephaly. Comparison by Western blot of FGF-2 transgenic mice to nontransgenic littermates showed expression of human FGF-2 protein in all major organs and tissues examined including brain, heart, lung, liver, kidney, spleen, and skeletal muscle; however, different molar ratios of FGF-2 protein isoforms were observed between different organs and tissues. Some tissues preferentially synthesize larger isoforms of FGF-2 while other tissues produce predominantly smaller 18-kDa FGF-2. Translation of the high molecular weight isoforms initiates from unconventional CUG codons and translation of the 18-kDa isoform initiates from an AUG codon in the FGF-2 mRNA. Thus the Western blot data from the FGF-2 transgenic mice suggest that tissue-specific expression of FGF-2 isoforms is regulated translationally. 相似文献
57.
Lee Alan Dugatkin David Sloan Wilson Livingston Farrand III Richard T. Wilkens 《Evolutionary ecology》1994,8(4):431-437
Summary In a prior study we combined game theory and inclusive fitness models to examine whether the guarded altruism that can evolve among non-relatives (tit for tat, TFT) might also evolve among close relatives, supplanting unconditional altruism. In most cases, TFT replaced unconditional altruism in family-structured models. Even when TFT is selected at a single locus, however, by withholding altruism from non-reciprocating relatives it may qualify as an outlaw from the standpoint of modifier genes at other loci. Here we examine this possibility with a series of haploid, two-locus models in which a modifier gene transforms TFT into unconditional altruism. The modifier allele spreads to fixation whenever Hamilton's Rule is satisfied, resulting in an unconditional altruist replacing the TFT strategy. As such, TFT may be regarded as an outlaw vulnerable to suppression by alleles at other loci. 相似文献
58.
Since the positive charge on the lysine residues plays an important role in the receptor recognition ability of oLH, the hormonotoxin has been synthesised with the use of 2-iminothiolane HC1 (2IT) and N-Succinimidyl-3-(2-pyridyldithio)-propionate (SPDP). The oLH activated with 2IT (oLH-10) was then mixed with SPDP activated gelonin (gelonin-30) in order to obtain a oLH-S-S-gelonin hormonotoxin. The conjugation mixture containing hormonotoxin was purified by gel-filtration chromatography according to the molecular weight and a complete physico-chemical, immunochemical and biochemical analysis were performed. The linkage occured through the -NH2 groups of -subunit of oLH as judged from RP-HPLC analysis. A 11 (oLH:gelonin) molar ratio was obtained when determined with the use of several techniques. The hormonotoxins retained substantial receptor binding, steroidogenic activity and immunoreactivity. The competitive displacement analysis indicate that the binding occurs via the hormone part leaving the gelonin free which was probed with the gelonin antibodies. The presently described (C150A-02, C160A-02 and C170A-02) hormonotoxins exhibited higher receptor binding and toxicity to the target cells than the hormonotoxins prepared with the use of SPDP only. Therefore it is concluded that higher receptor binding and cytotoxicity may be due to the retention of positive charge on the lysine residues of oLH which was preserved during the conjugation process.Abbreviations BSA
Bovine Serum Albumin
- CMC
Carboxy methyl Cellulose
- DTT
Dithiothreitol
- DMEM
Dulbeco's Modified Eagle's Medium
- DTNB
Ellman's reagent [5,5-dithio-bis-(2-nitrobenzoic acid)]
- EDTA
Ethylenediaminetetraacetic acid
- FPLC
Fast Protein Liquid Chromatography
- FCA
Freund's Complete Adjuvant
- FCS
Fetal Calf Serum
- Gelonin-30
Gelonin modified by SPDP
- GnRH
Gonadotropin-Releasing Hormone
- Gelonin-SPDP
SPDP modified derivative of gelonin
- HEPES
(N-[2-hydroxyethyl] piperazine-N-[-2-ethanesulphonic acid])
- IFA
Incomplete Freund's Adjuvant
- 2IT
2-Iminothiolane
- IODOGEN
1,3,4,6-tetrachloro 3,6-diphenylglycouril
- oLH
Ovine Luteinizing Hormone
- oLH-SPDP
SPDP modified derivative of oLH
- oLH-10
oLH modified by 2IT
- oLH2IT
Molar ratio of oLH and 2IT
- PDP
2-Pyridyl-dithiopropionate
- PAP
Pokeweed Antiviral Protein
- RIP
Ribosome Inactivating Protein
- RP-HPLC
Reverse-Phase High Performance Liquid Chromatography
- RPMI
Roswell Park Memorial Institute
- RIA
Radioimmunoassay
- RRA
Radioreceptor Assay
- SPDP
N-Succinimidyl-3(2-pyridyldithio)propionate
- SDS-PAGE
Sodium Dodecyl Sulphate-Polyacrylamide Gel Electrophoresis
- TCA
Trichloroacetic acid
- TFA
Trifluroacetic acid 相似文献
59.
R. Z. German D. W. Hertweck J. E. Sirianni D. R. Swindler 《American journal of physical anthropology》1994,93(3):373-380
Somatic growth is not a simple linear process with a constant rate of growth. The most successful attempts to quantify growth as a function of age or size have employed nonlinear techniques. Sexual dimorphism of primate growth, weight vs. age, was examined using nonlinear models with Sirianni and Swindler's ([1985] Growth and Development of the Pigtailed Macaque, Boca Raton, FL: CRC Press) growth data on the pigtailed macaque (Macaca nemestrina). The best fit of several exponential growth models was the Gompertz curve: Different multiple phase models were also fit, where each phase represents a distinct exponential component. The two-phase models proved to be the best (R2 = .0.84 for females, 0.91 for males), suggesting that there are two growth spurts, one in infancy and one at puberty. The timing of the beginning and end of the first spurt is the same in males and females, but the rate, and value of the asymptote for this phase, is greater in males. The timing of the second spurt is earlier, and the rate of growth for this spurt is smaller in females than males. The sexual dimorphism in these species is not a simple rate change, but a complex interaction of timing and rate over the entire period of growth. It would be impossible to separate these entities with a linear, polynomial, or single-phase model of the data. While these data and results complement much of the existing work on adult dimorphism, they also emphasize the vital role that ontogenetic data have in elucidating the underlying evolutionary mechanisms that generate sexual dimorphism. © 1994 Wiley-Liss, Inc. 相似文献
60.
Linkage disequilibrium between the FES, D15S127, and BLM loci in Ashkenazi Jews with Bloom syndrome. 总被引:4,自引:4,他引:0
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N. A. Ellis A. M. Roe J. Kozloski M. Proytcheva C. Falk J. German 《American journal of human genetics》1994,55(3):453-460
Bloom syndrome (BS) is more common in the Ashkenazi Jewish than in any other population. Approximately 1 in 110 Ashkenazi Jews carries blm, the BS mutation. The locus mutated in BS, BLM, maps to chromosome subband 15q26.1, tightly linked to the proto-oncogene FES. We have investigated the basis for the increased frequency of blm in the Ashkenazim by genotyping polymorphic microsatellite loci tightly linked to BLM in affected and unaffected individuals from Ashkenazi Jewish and non-Ashkenazi populations. A striking association of the C3 allele at FES with blm (delta = .422; p = 5.52 x 10(-7)) and of the 145-bp and 147-bp alleles at D15S127 with blm (delta = .392 and delta = .483, respectively; p = 2.8 x 10(-5) and p = 5.4 x 10(-7), respectively) was detected in Ashkenazi Jews with BS. This linkage disequilibrium constitutes strong support for a founder-effect hypothesis: the chromosome in the hypothetical founder who carried blm also carried the C3 allele at FES and either the 145-bp or the 147-bp allele at D15S127. 相似文献