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61.
Isaure Chauvot de Beauchene Sjoerd J. de Vries Martin Zacharias 《PLoS computational biology》2016,12(1)
Protein-RNA docking is hampered by the high flexibility of RNA, and particularly single-stranded RNA (ssRNA). Yet, ssRNA regions typically carry the specificity of protein recognition. The lack of methodology for modeling such regions limits the accuracy of current protein-RNA docking methods. We developed a fragment-based approach to model protein-bound ssRNA, based on the structure of the protein and the sequence of the RNA, without any prior knowledge of the RNA binding site or the RNA structure. The conformational diversity of each fragment is sampled by an exhaustive RNA fragment library that was created from all the existing experimental structures of protein-ssRNA complexes. A systematic and detailed analysis of fragment-based ssRNA docking was performed which constitutes a proof-of-principle for the fragment-based approach. The method was tested on two 8-homo-nucleotide ssRNA-protein complexes and was able to identify the binding site on the protein within 10 Å. Moreover, a structure of each bound ssRNA could be generated in close agreement with the crystal structure with a mean deviation of ~1.5 Å except for a terminal nucleotide. This is the first time a bound ssRNA could be modeled from sequence with high precision. 相似文献
62.
The aim of this experiment was to evaluate the effects of an intracerebroventricular (icv) injection of prostaglandin E1 (PGE1) on the sympathetic activation and the thermogenic changes in rats with acute lesions of the ventromedial hypothalamus (VMH). Four groups of six Sprague-Dawley male rats were anesthetized with ethyl-urethane. The firing rate of the sympathetic nerves innervating the interscapular brown adipose tissue (IBAT) and the colonic and IBAT temperatures were monitored both before and after one of the following treatments: 1) VMH lesion plus icv injection of PGE1 (500 ng); 2) VMH lesion plus icv injection of saline; 3) sham lesion plus icv injection of PGE1; and 4) sham lesion plus icv injection of saline. PGE1 induced an increase in the firing rate of IBAT nerves and the colonic and IBAT temperatures. These effects were reduced by VMH lesion. The findings indicate that acute lesions of the VMH reduce the effects of PGE1 and seem to suggest a possible role played by the VMH in the control of the sympathetic activation and the thermogenic changes during PGE1 hyperthermia. 相似文献
63.
Multiple haplotypes from each of three nuclear loci were isolated and
sequenced from geographic populations of the American oyster, Crassostrea
virginica. In tests of alternative phylogeographic hypotheses for this
species, nuclear gene genealogies constructed for these haplotypes were
compared to one another, to a mitochondrial gene tree, and to patterns of
allele frequency variation in nuclear restriction site polymorphisms
(RFLPs) and allozymes. Oyster populations from the Atlantic versus the Gulf
of Mexico are not reciprocally monophyletic in any of the nuclear gene
trees, despite considerable genetic variation and despite large allele
frequency differences previously reported in several other genetic assays.
If these populations were separated vicariantly in the past, either
insufficient time has elapsed for neutral lineage sorting to have achieved
monophyly at most nuclear loci, or balancing selection may have inhibited
lineage extinction, or secondary gene flow may have moved haplotypes
between regions. These and other possibilities are examined in light of
available genetic evidence, and it is concluded that no simple explanation
can account for the great variety of population genetic patterns across
loci displayed by American oysters. Regardless of the source of this
heterogeneity, this study provides an empirical demonstration that
different sequences of DNA within the same organismal pedigree can have
quite different phylogeographic histories.
相似文献
64.
65.
Eric J. McElroy Kristina M. Hill-Spanik Vincent A. Connors Isaure de Buron 《Invertebrate Biology》2023,142(2):e12399
Cryptic species of coquina clams Donax fossor and D. variabilis carry the hydroid epibiont Lovenella gracilis and are infected with metacercariae of the monorchiid parasites Lasiotocus trachinoti and L. choanura. The associations among this host–epibiont–parasite system were investigated. Fifty clams were collected at low tide over 3 days in June 2020 in South Carolina from each of three groups: clams with no hydroid from the upper intertidal zone and clams with and without hydroids from the swash zone. Clams were measured, identified using a newly developed PCR-RFLP, and examined for infection by metacercariae. Parasites were identified based on cercarial morphology and on metacercariae habitat in the clams. D. fossor was most often found in the swash zone and D. variabilis in the upper intertidal zone. The hydroid was most often associated with D. fossor, which was more infected by both digeneans than D. variabilis. Mean abundance of metacercariae of L. choanura was higher than that of L. trachinoti in both clams and increased over time for both parasites, because higher infection was correlated with larger clams. Greater time spent in the water by individuals of D. fossor appears to best explain these results, with the presence of the hydroids also being associated with higher infection by metacercariae in this coquina. Integration of D. variabilis in both digenean life cycles appears to lead to a positive outcome for the parasites as prevalence and abundance of infection were high; however, because D. variabilis is most frequent in the upper intertidal, more emersed, zone, it is likely deleterious to the epibiont to establish on this clam. 相似文献
66.
67.
Crustacean and cheliceratan hemocyanins (oxygen-transport proteins) and
insect hexamerins (storage proteins) are homologous gene products, although
the latter do not bind oxygen and do not possess the copper- binding
histidines present in the hemocyanins. An alignment of 19 amino acid
sequences of hemocyanin subunits and insect hexamerins was made, based on
the conservation of elements of secondary structure observed in X-ray
structures of two hemocyanin subunits. The alignment was analyzed using
parsimony and neighbor-joining methods. Results provide strong indications
for grouping together the sequences of the 2 crustacean hemocyanin
subunits, the 5 cheliceratan hemocyanin subunits, and the 12 insect
hexamerins. Within the insect clade, four methionine- rich proteins, four
arylphorins, and two juvenile hormone-suppressible proteins from
Lepidoptera, as well as two dipteran proteins, form four separate groups.
In the absence of an outgroup sequence, it is not possible to present
information about the ancestral state from which these proteins are
derived. Although this family of proteins clearly consists of homologous
gene products, there remain striking differences in gene organization and
site of biosynthesis of the proteins within the cell. Because studies on
18S and 12S rRNA sequences indicate a rather close relationship between
insects and crustaceans, we propose that hemocyanin is the ancestral
arthropod protein and that insect hexamerins lost their copper-binding
capability after divergence of the insects from the crustaceans.
相似文献
68.
69.
This paper looked at the leaf architecture characteristics of Vachellia tortilis to determine if either there is or not an effect of the tropic line on plants. Vachellia tortilis leaves were sampled along a national road (N1) in Limpopo province. Sampling points were set 10 km apart away from the Tropic of Capricon in opposite directions. Leaf morphology revealed that leaves of V. tortilis are bipinnately compound with alternate arrangement. The venation pattern of the pinnules was eucamptodromus and brochidodromous with imperfect reticulation. Areoles were imperfect and pentagonal or irregular in shape. 相似文献
70.
Jasmin Ana Luiza M Torres Henrique MP Nunes Juliana A Passipieri Linda A Jelicks Emerson L Gasparetto David C Spray Antonio C Campos de Carvalho Rosalia Mendez-Otero 《Journal of nanobiotechnology》2011,9(1):4