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41.
Francisco M. Ortu?o Olga Valenzuela Hector Pomares Fernando Rojas Javier P. Florido Jose M. Urquiza Ignacio Rojas 《Nucleic acids research》2013,41(1):e26
Multiple sequence alignments (MSAs) have become one of the most studied approaches in bioinformatics to perform other outstanding tasks such as structure prediction, biological function analysis or next-generation sequencing. However, current MSA algorithms do not always provide consistent solutions, since alignments become increasingly difficult when dealing with low similarity sequences. As widely known, these algorithms directly depend on specific features of the sequences, causing relevant influence on the alignment accuracy. Many MSA tools have been recently designed but it is not possible to know in advance which one is the most suitable for a particular set of sequences. In this work, we analyze some of the most used algorithms presented in the bibliography and their dependences on several features. A novel intelligent algorithm based on least square support vector machine is then developed to predict how accurate each alignment could be, depending on its analyzed features. This algorithm is performed with a dataset of 2180 MSAs. The proposed system first estimates the accuracy of possible alignments. The most promising methodologies are then selected in order to align each set of sequences. Since only one selected algorithm is run, the computational time is not excessively increased. 相似文献
42.
Despite the predicted purifying role of stabilising selection against variation in warning signals, many aposematic species exhibit high variation in their colour patterns. The maintenance of such variation is not well understood, but it has been suggested to be the result of an interaction between sexual and natural selection. This interaction could also facilitate the evolution of sexual dichromatism. Here we analyse in detail the colour patterns of the poison frog Dendrobates tinctorius and evaluate the possible correlates of the variability in aposematic signals in a natural population. Against the theoretical predictions of aposematism, we found that there is enormous intra-populational variation in colour patterns and that these also differ between the sexes: males have a yellower dorsum and bluer limbs than females. We discuss the possible roles of natural and sexual selection in the maintenance of this sexual dimorphism in coloration and argue that parental care could work synergistically with aposematism to select for yellower males. 相似文献
43.
Ángel Vale Danny Rojas Julio C. Álvarez Luis Navarro 《Botanical journal of the Linnean Society. Linnean Society of London》2013,172(3):345-357
The geographical distribution, population structure and pollination ecology are key aspects in the conservation and management of rare orchids. Here, we address these aspects and the main threats affecting the endangered Cuban orchid Broughtonia cubensis. This rewardless orchid is self‐compatible, but pollinator dependent. However, seed production can be negatively affected by insect‐mediated selfing. Three species of small bee (genera Ceratina and Lasioglossum) act as pollinators. As in the case of other nectarless orchids, we detected two species of plant producing large amounts of nectar in the area, the floral morphology of which closely resembles that of B. cubensis. The simultaneous flowering of these species could positively affect the reproductive success of B. cubensis. Nonetheless, the fitness of this orchid in natural conditions is low, possibly related to strong pollen limitation. To the problems arising from reduced fitness is added the fact that its historical distribution range has been greatly reduced in recent years. Throughout this study, we have detected dramatic reductions in the population sizes, in some cases as a result of human plundering, but also as a consequence of hurricanes. Based on the results of this study, we propose some guidelines to manage and conserve this orchid. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 345–357. 相似文献
44.
Gloria Arratia F. Augusto Chang G. Silvina Menu Marque Guido Rojas M. 《Studies on Neotropical Fauna and Environment》2013,48(3-4):157-194
A new genus of the family Trichomycteridae, Bullockia, and a new species of Trichomycterus are described. Bullockia gen. nov. is a monospecific and relict genus in the freshwaters of Chile. Trichomycterus mendozensis n. sp. is a freshwater relict from Argentina. Preliminary diagnoses of the subfamilies Pygidiinae and Nematogenyinae and the genera Trichomycterus, Hatcheria and Nematogenys are given. 相似文献
45.
Serine/threonine kinases and E2-ubiquitin conjugating enzymes in Planctomycetes: unexpected findings
The regulation of signal transduction by phosphorylation and ubiquitination is essential to ensure the correct behavior of eukaryotic cells. We searched for protein families involved in such signaling in several eukaryotic species and in a limited set of prokaryotes, where two members of the Planctomycetes phylum were included as they exhibit eukaryote-like features (Gemmata obscuriglobus and Pirellula staleyi). We identified sequences homologous to eukaryotic serine/threonine kinases (STKs) and E2-ubiquitin conjugating enzymes in the two Planctomycetes species. To extend these analyses to the Planctomycetes/Verrucomicrobia/Chlamydia super-phylum, we performed comparative analyses using domains from kinases, phosphatases and GTPases that serve as signaling signatures, and we analyzed their distributions. We found substantial differences in kinome densities with regards to other prokaryote clades and among the groups in the Planctomycetes/Verrucomicrobia/Chlamydia super-phylum. In addition, we identified the presence of classic eukaryotic E2-conjugating ubiquitin proteins in prokaryotes, these having previously believed to exist only in eukaryotes. Our phylogenetic analyses of the STKs signature domains and E2-enzymes suggest the existence of horizontal gene transfer. 相似文献
46.
In the city of Santiago (33°27'S70°38'W), Chile, an atmospheric pollen was monitored for three years using a volumetric Hirst-type pollen trap. The aims of the study were: to assess the pollen types present in the atmosphere, their actual concentrations and dynamics (means and maxima); to establish the pollen calendar for Santiago; and to analyze the aerobiologic characteristics distinguishing introduced and native taxa. Results show that atmospheric pollen mainly originates from the following taxa: Platanus , Poaceae, Acer , Cupressus , Chenopodiaceae, Urticaceae, Morus , Plantago and Oleaceae. For the most frequent pollen types graphs of their atmospheric presence constructed and a table with relevant yearly data for the three studied (July-June) is presented. It is concluded, that the airborne pollen is originating mainly from introduced taxa, many of which are considered allergenic. Native taxa showed no high concentrations. The highest aiborne pollen concentrations where observed in September, however, atmospheric pollen thought to be capable of causing pollinosis, where present during the whole year. The highest pollen concentrations are mostly from trees. 相似文献
47.
Ruth Goldschmidt Pablo M. Arce Omar M. Khdour Valérie C. Collin Sriloy Dey Jennifer Jaruvangsanti David M. Fash Sidney M. Hecht 《Bioorganic & medicinal chemistry》2013,21(4):969-978
Two new aza analogues of the neuroprotective agent idebenone have been synthesized and characterized. Their antioxidant activity, and ability to augment ATP levels have been evaluated in several different cell lines having suboptimal mitochondrial function. Both compounds were found to be good ROS scavengers, and to protect the cells from oxidative stress induced by glutathione depletion. The compounds were more effective than idebenone in neurodegenerative disease cells. These novel pyrimidinol derivatives were also shown to augment ATP levels in coenzyme Q10-deficient human lymphocytes. The more lipophilic side chains attached to the pyrimidinol redox core in these compounds resulted in less inhibition of the electron transport chain and improved antioxidant activity. 相似文献
48.
49.
Y-H Fan J Cheng S A Vasudevan J Dou H Zhang R H Patel I T Ma Y Rojas Y Zhao Y Yu H Zhang J M Shohet J G Nuchtern E S Kim J Yang 《Cell death & disease》2013,4(10):e867
Neuroblastoma (NB) is a common pediatric cancer and contributes to more than 15% of all pediatric cancer-related deaths. Unlike adult tumors, recurrent somatic mutations in NB, such as tumor protein 53 (p53) mutations, occur with relative paucity. In addition, p53 downstream function is intact in NB cells with wild-type p53, suggesting that reactivation of p53 may be a viable therapeutic strategy for NB treatment. Herein, we report that the ubiquitin-specific protease 7 (USP7) inhibitor, , potently induces apoptosis in NB cells with an intact USP7-HDM2-p53 axis but not in NB cells with mutant p53 or without human homolog of MDM2 (HDM2) expression. In this study, we found that P22077 stabilized p53 by inducing HDM2 protein degradation in NB cells. P22077 also significantly augmented the cytotoxic effects of doxorubicin (Dox) and etoposide (VP-16) in NB cells with an intact USP7-HDM2-p53 axis. Moreover, P22077 was found to be able to sensitize chemoresistant LA-N-6 NB cells to chemotherapy. In an in vivo orthotopic NB mouse model, P22077 significantly inhibited the xenograft growth of three NB cell lines. Database analysis of NB patients shows that high expression of USP7 significantly predicts poor outcomes. Together, our data strongly suggest that targeting USP7 is a novel concept in the treatment of NB. USP7-specific inhibitors like P22077 may serve not only as a stand-alone therapy but also as an effective adjunct to current chemotherapeutic regimens for treating NB with an intact USP7-HDM2-p53 axis. P22077相似文献
50.
Leonida?Fusani Francesca?Coccon Alfonso?Rojas Mora Wolfgang?GoymannEmail author 《Frontiers in zoology》2013,10(1):79