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91.
Protein-mediated DNA looping, such as that induced by the lactose repressor (LacI) of Escherichia coli, is a well-known gene regulation mechanism. Although researchers have given considerable attention to DNA looping by LacI, many unanswered questions about this mechanism, including the role of protein flexibility, remain. Recent single-molecule observations suggest that the two DNA-binding domains of LacI are capable of splaying open about the tetramerization domain into an extended conformation. We hypothesized that if recent experiments were able to reveal the extended conformation, it is possible that such structures occurred in previous studies as well. In this study, we tested our hypothesis by reevaluating two classic in vitro binding assays using a computational rod model of DNA. The experiments and computations evaluate the looping of both linear DNA and supercoiled DNA minicircles over a broad range of DNA interoperator lengths. The computed energetic minima align well with the experimentally observed interoperator length for optimal loop stability. Of equal importance, the model reveals that the most stable loops for linear DNA occur when LacI adopts the extended conformation. In contrast, for DNA minicircles, optimal stability may arise from either the closed or the extended protein conformation depending on the degree of supercoiling and the interoperator length. 相似文献
92.
目的:建立丙型肝炎病毒NS3/4A丝氨酸蛋白酶体内活性评价模型。方法:利用NS4A/B是NS3/4A丝氨酸蛋白酶作用底物的特性,构建融合基因NS3/NS4A/B-SEAP,底物片段NS4A/B插在NS3/4A和人分泌性碱性磷酸酶(SEAP)之间,融合基因表达后SEAP的分泌依赖于有活性的NS3/4A在NS4A/B位点的切割。将含融合基因的质粒NS3/4A(△4AB)SEAP通过水动力转染技术转染到小鼠体内,检测小鼠血清中SEAP的活性,高活性的SEAP是该评价体系成立的证据。结果与结论:在瞬时表达NS3/4A的小鼠血清中检测到了高活性的SEAP,建立了可用于评价抗NS3/4A的小鼠体内瞬时模型。 相似文献
93.
Camarodont sea urchins possess a rapidly evolving actin gene family whose
members are expressed in distinct cell lineages in a developmentally
regulated fashion. Evolutionary changes in the actin gene family of
echinoids include alterations in number of family members, site of
expression, and gene linkage, and a dichotomy between rapidly and slowly
evolving isoform-specific 3' untranslated regions. We present sequence
comparisons and an analysis of the actin gene family in two congeneric sea
urchins that develop in radically different modes, Heliocidaris
erythrogramma and H. tuberculata. The sequences of several actin genes from
the related species Lytechinus variegatus are also presented. We compare
the features of the Heliocidaris and Lytechinus actin genes to those of the
the actin gene families of other closely related sea urchins and discuss
the nature of the evolutionary changes among sea urchin actins and their
relationship to developmental mode.
相似文献
94.
The phytochrome gene family in grasses (Poaceae): a phylogeny and evidence that grasses have a subset of the loci found in dicot angiosperms 总被引:13,自引:2,他引:11
The phytochrome nuclear gene family encodes photoreceptor proteins that
mediate developmental responses to red and far red light throughout the
life of the plant. From studies of the dicot flowering plant Arabidopsis,
the family has been modeled as comprising five loci, PHYA- PHYE. However,
it has been shown recently that the Arabidopsis model may not completely
represent some flowering plant groups because additional PHY loci related
to PHYA and PHYB of Arabidopsis apparently have evolved independently
several times in dicots, and monocot flowering plants may lack orthologs of
PHYD and PHYE of Arabidopsis. Nonetheless, the phytochrome nucleotide data
were informative in a study of organismal evolution because the loci occur
as single copy sequences and appear to be evolving independently. We have
continued our investigation of the phytochrome gene family in flowering
plants by sampling extensively in the grass family. The phytochrome nuclear
DNA data were cladistically analyzed to address the following questions:
(1) Are the data consistent with a pattern of differential distribution of
phytochrome genes among monocots and higher dicots, with homologs of PHYA,
B, C, D, and E present in higher dicots, but of just PHYA, B, and C in
monocots, and (2) what phylogenetic pattern within Poaceae do they reveal?
Results of these analyses, and of Southern blot experiments, are consistent
with the observation that the phytochrome gene family in grasses comprises
the same subset of loci detected in other monocots. Furthermore, for
studies of organismal phylogeny in the grass family, the data are shown to
provide significant support for relationships that are just weakly resolved
by other data sets.
相似文献
95.
Comparison of the effects of concentration, pH and anion species on astringency and sourness of organic acids 总被引:3,自引:1,他引:3
The separate effects of concentration, pH and anion species on intensity of
sourness and astringency of organic acids were evaluated. Judges rated
sourness and astringency intensity of lactic, malic, tartaric and citric
acid solutions at three levels of constant pH varying in normality and at
three levels of constant concentration varying in pH. To assess the
comparative sourness and astringency of the organic acid anions of study,
binary acid solutions matched in pH and titratable acidity were also rated.
As pH was decreased in equinormal solutions, both sourness and astringency
increased significantly (P < 0.001). By contrast, as the normality of
the equi-pH solutions was increased, only sourness demonstrated significant
increases (P < 0.001) while astringency remained constant or decreased
slightly. At the lowest normality tested, all solutions were more
astringent than sour (P < 0.05). Although lactic acid was found to be
significantly more sour than citric acid (P < 0.05), no other sourness
or astringency differences among the organic acid anions were noted. This
study demonstrates for the first time that astringency elicited by acids is
a function of pH and not concentration or anion species, and confirms that
sourness is independently influenced by concentration, pH and anion species
of the acid.
相似文献
96.
Mitchell J. Brunet Kevin L. Monteith Katey S. Huggler Justin G. Clapp Daniel J. Thompson Patrick W. Burke Mark Zornes Patrick Lionberger Miguel Valdez Joseph D. Holbrook 《Ecology and evolution》2022,12(2)
Successfully perceiving risk and reward is fundamental to the fitness of an animal, and can be achieved through a variety of perception tactics. For example, mesopredators may “directly” perceive risk by visually observing apex predators, or may “indirectly” perceive risk by observing habitats used by predators. Direct assessments should more accurately characterize the arrangement of risk and reward; however, indirect assessments are used more frequently in studies concerning the response of GPS‐marked animals to spatiotemporally variable sources of risk and reward. We investigated the response of a mesopredator to the presence of risk and reward created by an apex predator, where risk and reward likely vary in relative perceptibility (i.e., degree of being perceptible). First, we tested whether coyotes (Canis latrans) use direct or indirect assessments to navigate the presence of mountain lions (Puma concolor; risk) and kills made by mountain lions (reward) in an area where coyotes were a common prey item for mountain lions. Second, we assessed the behavioral response of coyotes to direct encounters with mountain lions. Third, we evaluated spatiotemporal use of carrion by coyotes at kills made by mountain lions. Indirect assessments generally outperformed direct assessments when integrating analyses into a unified framework; nevertheless, our ability to detect direct perception in navigating to mountain lion kills was likely restricted by scale and sampling limitations (e.g., collar fix rates, unsampled kill sites). Rather than responding to the risk of direct encounters with mountain lions, coyotes facilitated encounters by increasing their movement rate, and engaged in risky behavior by scavenging at mountain lion kills. Coyotes appear to mitigate risk by using indirect perception to avoid mountain lions. Our predator–predator interactions and insights are nuanced and counter to the conventional predator–prey systems that have generated much of the predation risk literature. 相似文献
97.
Degradation of extracellular matrix by mouse trophoblast outgrowths: a model for implantation 总被引:7,自引:6,他引:1 下载免费PDF全文
During implantation the embryo attaches to the endometrial surface and trophoblast traverses the uterine epithelium, anchoring in the uterine connective tissue. To determine whether trophoblast can facilitate invasion of the uterus by degrading components of normal uterine extracellular matrix, mouse blastocysts were cultured on a radio-labeled extracellular matrix that contained glycoproteins, elastin, and collagen. The embryos attached to the matrix, and trophoblast spread over the surface. Starting on day 5 of culture there was a release of labeled peptides into the medium. The radioactive peptides released from the matrix by the embryos had molecular weights ranging from more than 25,000 to more than 200. By day 7 there were areas where individual trophoblast cells had separated from one another, revealing the underlying substratum that was cleared of matrix. When trophoblast cells were lysed with NH(4)OH on day 8, it was apparent that the area underneath the trophoblast outgrowth had been cleared of matrix. Scanning electron microscopy and time-lapse cinemicrography confirmed that the digestion of matrix was highly localized, taking place only underneath the trophoblast, with no evidence of digestion of the matrix beyond the periphery of the trophoblast outgrowth. The sharp boundaries of degredation observed may be due to localized proteinase secretion by trophoblast, to membrane proteinases on the surface of trophoblast, or to endocytosis. Digestion of the matrix was not dependent on plasminogen, thus ruling out a role for plasminogen activator. Digestion was not inhibited by a variety of hormones and inhibitors, including progesterone, 17β-estradiol, leupeptin, EDTA, colchicine, NH(4)Cl, or ε-aminocaproic acid. This system of culturing embryos on extracellular matrix may be useful in determining the processes that regulate trophoblast migration and invasion into the maternal tissues during implantation.0 相似文献
98.
Partial 18S rRNA sequences of five chelicerate arthropods plus a
crustacean, myriapod, insect, chordate, echinoderm, annelid, and
platyhelminth were compared. The sequence data were used to infer phylogeny
by using a maximum-parsimony method, an evolutionary-distance method, and
the evolutionary-parsimony method. The phylogenetic inferences generated by
maximum-parsimony and distance methods support both monophyly of the
Arthropoda and monophyly of the Chelicerata within the Arthropoda. These
results are congruent with phylogenies based on rigorous cladistic analyses
of morphological characters. Results support the inclusion of the
Arthropoda within a spiralian or protostome coelomate clade that is the
sister group of a deuterostome clade, refuting the hypothesis that the
arthropods represent the "primitive" sister group of a protostome coelomate
clade. Bootstrap analyses and consideration of all trees within 1% of the
length of the most parsimonious tree suggest that relationships between the
nonchelicerate arthropods and relationships within the chelicerate clade
cannot be reliably inferred with the partial 18S rRNA sequence data. With
the evolutionary-parsimony method, support for monophyly of the Arthropoda
is found in the majority of the combinations analyzed if the coelomates are
used as "outgroups." Monophyly of the Chelicerata is supported in most
combinations assessed. Our analyses also indicate that the
evolutionary-parsimony method, like distance and parsimony, may be biased
by taxa with long branches. We suggest that a previous study's inference of
the Arthropoda as paraphyletic may be the result of (a) having two few
arthropod taxa available for analysis and (b) including long-branched taxa.
相似文献
99.
100.
Deuterostome phylogeny and the sister group of the chordates: evidence from molecules and morphology 总被引:13,自引:3,他引:10
Complete coding regions of the 18S rRNA gene of an enteropneust
hemichordate and an echinoid and ophiuroid echinoderm were obtained and
aligned with 18S rRNA gene sequences of all major chordate clades and four
outgroups. Gene sequences were analyzed to test morphological character
phylogenies and to assess the strength of the signal. Maximum- parsimony
analysis of the sequences fails to support a monophyletic Chordata; the
urochordates form the sister taxon to the hemichordates, and together this
clade plus the echinoderms forms the sister taxon to the cephalochordates
plus craniates. Decay, bootstrap, and tree-length distribution analyses
suggest that the signal for inference of dueterostome phylogeny is weak in
this molecule. Parsimony analysis of morphological plus molecular
characters supports both monophyly of echinoderms plus enteropneust
hemichordates and a sister group relationship of this clade to chordates.
Evolutionary parsimony does not support chordate monophyly.
Neighbor-joining, Fitch-Margoliash, and maximum-likelihood analyses support
a chordate lineage that is the sister group to an
echinoderm-plus-hemichordate lineage. The results illustrate both the
limitations of the 18S rRNA molecule alone for high- level phylogeny
inference and the importance of considering both molecular and
morphological data in phylogeny reconstruction.
相似文献