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51.
Background
Biology is experiencing a gradual but fast transformation from a laboratory-centred science towards a data-centred one. As such, it requires robust data engineering and the use of quantitative data analysis methods as part of database curation. This paper focuses on G protein-coupled receptors, a large and heterogeneous super-family of cell membrane proteins of interest to biology in general. One of its families, Class C, is of particular interest to pharmacology and drug design. This family is quite heterogeneous on its own, and the discrimination of its several sub-families is a challenging problem. In the absence of known crystal structure, such discrimination must rely on their primary amino acid sequences.Methods
We are interested not as much in achieving maximum sub-family discrimination accuracy using quantitative methods, but in exploring sequence misclassification behavior. Specifically, we are interested in isolating those sequences showing consistent misclassification, that is, sequences that are very often misclassified and almost always to the same wrong sub-family. Random forests are used for this analysis due to their ensemble nature, which makes them naturally suited to gauge the consistency of misclassification. This consistency is here defined through the voting scheme of their base tree classifiers.Results
Detailed consistency results for the random forest ensemble classification were obtained for all receptors and for all data transformations of their unaligned primary sequences. Shortlists of the most consistently misclassified receptors for each subfamily and transformation, as well as an overall shortlist including those cases that were consistently misclassified across transformations, were obtained. The latter should be referred to experts for further investigation as a data curation task.Conclusion
The automatic discrimination of the Class C sub-families of G protein-coupled receptors from their unaligned primary sequences shows clear limits. This study has investigated in some detail the consistency of their misclassification using random forest ensemble classifiers. Different sub-families have been shown to display very different discrimination consistency behaviors. The individual identification of consistently misclassified sequences should provide a tool for quality control to GPCR database curators.52.
Włodzimierz Jędrzejewski Wojciech Branicki Claudia Veit Ivica MeĐugorac Małgorzata Pilot Aleksei N. Bunevich Bogumiła Jędrzejewska Krzysztof Schmidt Jörn Theuerkauf Henryk Okarma Roman Gula Lucyna Szymura Martin Förster 《Acta theriologica》2005,50(1):3-22
A population of grey wolvesCanis lupus Linnaeus, 1758 inhabiting Bia?owie?a Primeval Forest (BPF) on the Polish-Belarussian border has recovered after near extermination in the 1970s. Currently, it is intensively hunted in the Belarussian part of BPF and protected in the Polish part. We used a combination of molecular analysis, radiotracking, and field observation to study genetic diversity of the population after natural recolonisation and the consequences of heavy hunting for the genetic composition and social structure of wolf packs. Both microsatellite and mtDNA analyses revealed high genetic diversity. For 29 individuals and 20 microsatellite loci, the mean expected heterozygosity was 0.733. Four mtDNA haplotypes were found. Three of them had earlier been described from Europe. Their geographic distribution suggests that wolves recolonising BPF immigrated mainly from the north-east, and less effectively from the east and south-east. We traced the composition of 6 packs for a total of 26 pack-years. Packs were family units (a breeding pair with offspring) with occasional adoption of unrelated adult males, which occurred more frequently in packs living in the Belarussian part of the BPF, due to heavy hunting and poaching. Breeding pairs were half-sibs or unrelated wolves. Pair-bonds in the breeding pair lasted from 1 to 4 years and usually broke by the death of one or both mates. Successors of breeding females were their daughters, while a successor of a breeding male could be either his son or an alien wolf. As is evident from Bia?owie?a’s wolves, high genetic diversity may result from immigration of outside individuals, which are easily recruited to a heavily exploited local population. 相似文献
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Orlova Yuliya V. Sergienko Olga V. Khalilova Lyudmila A. Voronkov Alexander S. Fomenkov Artem A. Nosov Alexander V. Popova Larissa G. Shuvalov Aleksei V. Ryabova Anastasia V. Balnokin Yuri V. 《In vitro cellular & developmental biology. Plant》2019,55(4):359-370
In Vitro Cellular & Developmental Biology - Plant - The involvement of endocytosis in Na+ internalization by suspension-cultured Arabidopsis thaliana (L.) Heynh. cells under salt stress was... 相似文献
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Shadyro OI Sosnovskaya AA Edimecheva IP Grintsevich IB Lagutin PY Alekseev AV Kazem K 《Free radical research》2005,39(7):713-718
Effects of vitamins B, C, E, K and P, as well as coenzymes Q, on formation of final products of radiation-induced free-radical transformations of ethanol, ethylene glycol, alpha-methylglycoside and glucose in aqueous solutions were studied. Based on the obtained results, it can be concluded that there are substances among vitamins and coenzymes that effectively interact with alpha-hydroxyl-containing radicals. In the presence of these substances, recombination reactions of alpha-hydroxyalkyl radicals and fragmentation of alpha-hydroxy-beta-substituted organic radicals are suppressed. It has been established that the observed effects are due to the ability of the vitamins and coenzymes under study to either oxidize alpha-hydroxyl-containing radicals yielding the respective carbonyl compounds or reduce them into the initial molecules. 相似文献
55.
Koskinen H Pehkonen P Vehniäinen E Krasnov A Rexroad C Afanasyev S Mölsa H Oikari A 《Biochemical and biophysical research communications》2004,320(3):745-753
We used high-density cDNA microarray in studies of responses of rainbow trout fry at sublethal ranges of beta-naphthoflavone, cadmium, carbon tetrachloride, and pyrene. The differentially expressed genes were grouped by the functional categories of Gene Ontology. Significantly different response to the studied compounds was shown by a number of classes, such as cell cycle, apoptosis, signal transduction, oxidative stress, subcellular and extracellular structures, protein biosynthesis, and modification. Cluster analysis separated responses to the contaminants at low and medium doses, whereas at high levels the adaptive reactions were masked with general unspecific response to toxicity. We found enhanced expression of many mitochondrial proteins as well as genes involved in metabolism of metal ions and protein biosynthesis. In parallel, genes related to stress and immune response, signal transduction, and nucleotide metabolism were down-regulated. We performed computer-assisted analyses of Medline abstracts retrieved for each compound, which helped us to indicate the expected and novel findings. 相似文献
56.
Inna?E.?PristyazhnyukEmail authorView authors OrcID profile
return OK on get Aleksei?G.?Menzorov 《Protoplasma》2018,255(2):439-449
Ring chromosomes (RCs) are circular DNA molecules, which occur rarely in eukaryotic nuclear genomes. Lilian Vaughan Morgan first described them in the fruit fly. Human embryos very seldom have RCs, about 1:50,000. Carriers of RCs may have varying degrees of symptoms, from healthy phenotype to serious pathologies in physical and intellectual development. Many authors describe common symptoms of RC presence: short stature and some developmental delay that could be described as a “ring chromosome syndrome.” As a rule, RCs arise de novo through the end-joining of two DNA double-strand breaks, telomere-subtelomere junction, or inv dup del rearrangement in both meiosis and mitosis. There are family cases of RC inheritance. The presence of RCs causes numerous secondary chromosome rearrangements in vivo and in vitro. RCs can change their size, become lost, or increase their copy number and cause additional deletions, duplication, and translocations, affecting both RCs and other chromosomes. In this review, we examine RC inheritance, instability, mechanisms of formation, and potential clinical applications of artificially created RCs for large-scale chromosome rearrangement treatment. 相似文献
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Elisa Bellucci Orlando Mario Aguilar Saleh Alseekh Kirstin Bett Creola Brezeanu Douglas Cook Lucía De la Rosa Massimo Delledonne Denise F. Dostatny Juan J. Ferreira Valérie Geffroy Sofia Ghitarrini Magdalena Kroc Shiv Kumar Agrawal Giuseppina Logozzo Mario Marino Tristan Mary-Huard Phil McClean Vladimir Meglič Tamara Messer Frédéric Muel Laura Nanni Kerstin Neumann Filippo Servalli Silvia Străjeru Rajeev K. Varshney Marta W. Vasconcelos Massimo Zaccardelli Aleksei Zavarzin Elena Bitocchi Emanuele Frontoni Alisdair R. Fernie Tania Gioia Andreas Graner Luis Guasch Lena Prochnow Markus Oppermann Karolina Susek Maud Tenaillon Roberto Papa 《The Plant journal : for cell and molecular biology》2021,108(3):646-660
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Laura Martinez-Rubio ?ystein Evensen Aleksei Krasnov Sven Martin J?rgensen Simon Wadsworth Kari Ruohonen Jose LG Vecino Douglas R Tocher 《BMC genomics》2014,15(1)