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991.
COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations 总被引:3,自引:0,他引:3
MOTIVATION: Determining orthology relations among genes across multiple genomes is an important problem in the post-genomic era. Identifying orthologous genes can not only help predict functional annotations for newly sequenced or poorly characterized genomes, but can also help predict new protein-protein interactions. Unfortunately, determining orthology relation through computational methods is not straightforward due to the presence of paralogs. Traditional approaches have relied on pairwise sequence comparisons to construct graphs, which were then partitioned into putative clusters of orthologous groups. These methods do not attempt to preserve the non-transitivity and hierarchic nature of the orthology relation. RESULTS: We propose a new method, COCO-CL, for hierarchical clustering of homology relations and identification of orthologous groups of genes. Unlike previous approaches, which are based on pairwise sequence comparisons, our method explores the correlation of evolutionary histories of individual genes in a more global context. COCO-CL can be used as a semi-independent method to delineate the orthology/paralogy relation for a refined set of homologous proteins obtained using a less-conservative clustering approach, or as a refiner that removes putative out-paralogs from clusters computed using a more inclusive approach. We analyze our clustering results manually, with support from literature and functional annotations. Since our orthology determination procedure does not employ a species tree to infer duplication events, it can be used in situations when the species tree is unknown or uncertain. CONTACT: jothi@mail.nih.gov, przytyck@mail.nih.gov SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online. 相似文献
992.
We propose a novel approach to predict domain-domain interactions from a protein-protein interaction network. In our method we apply a parsimony-driven explanation of the network, where the domain interactions are inferred using linear programming optimization, and false positives in the protein network are handled by a probabilistic construction. This method outperforms previous approaches by a considerable margin. The results indicate that the parsimony principle provides a correct approach for detecting domain-domain contacts. 相似文献
993.
In spite of recent advances with experiments on animal models, strongyloidiasis, an infection caused by the nematode parasite Strongyloides stercoralis, has still been an elusive disease. Though endemic in some developing countries, strongyloidiasis still poses a threat to the developed world. Due to the peculiar but characteristic features of autoinfection, hyperinfection syndrome involving only pulmonary and gastrointestinal systems, and disseminated infection with involvement of other organs, strongyloidiasis needs special attention by the physician, especially one serving patients in areas endemic for strongyloidiasis. Strongyloidiasis can occur without any symptoms, or as a potentially fatal hyperinfection or disseminated infection. Th2 cell-mediated immunity, humoral immunity and mucosal immunity have been shown to have protective effects against this parasitic infection especially in animal models. Any factors that suppress these mechanisms (such as intercurrent immune suppression or glucocorticoid therapy) could potentially trigger hyperinfection or disseminated infection which could be fatal. Even with the recent advances in laboratory tests, strongyloidiasis is still difficult to diagnose. But once diagnosed, the disease can be treated effectively with antihelminthic drugs like Ivermectin. This review article summarizes a case of strongyloidiasis and various aspects of strongyloidiasis, with emphasis on epidemiology, life cycle of Strongyloides stercoralis, clinical manifestations of the disease, corticosteroids and strongyloidiasis, diagnostic aspects of the disease, various host defense pathways against strongyloidiasis, and available treatment options. 相似文献
994.
Background
Improvements in DNA sequencing technology and methodology have led to the rapid expansion of databases comprising DNA sequence, gene and genome data. Lower operational costs and heightened interest resulting from initial intriguing novel discoveries from genomics are also contributing to the accumulation of these data sets. A major challenge is to analyze and to mine data from these databases, especially whole genomes. There is a need for computational tools that look globally at genomes for data mining. 相似文献995.
996.
Mohd Fakharul Zaman Raja Yahya Zazali Alias Saiful Anuar Karsani 《The protein journal》2017,36(4):286-298
Salmonella typhimurium is an important biofilm-forming bacteria. It is known to be resistant to a wide range of antimicrobials. The present study was carried out to evaluate the effects of dimethyl sulfoxide (DMSO) against S. typhimurium biofilm and investigate whole-cell protein expression by biofilm cells following treatment with DMSO. Antibiofilm activities were assessed using pellicle assay, crystal violet assay, colony-forming unit counting and extracellular polymeric substance (EPS) matrix assay whilst differential protein expression was investigated using a combination of one dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis, tandem mass spectrometry and bioinformatics. Treatment with 32% DMSO inhibited pellicle formation, biofilm viability, biofilm biomass and several important components of EPS matrix. Subtractive protein profiling identified two unique protein bands (25.4 and 51.2 kDa) which were present only in control biofilm and not in 32% DMSO-treated biofilm. In turn, 29 and 46 proteins were successfully identified from the protein bands of 25.4 and 51.2 kDa respectively. Protein interaction network analysis identified several biological pathways to be affected, including glycolysis, PhoP–PhoQ phosphorelay signalling and flagellar biosynthesis. The present study suggests that DMSO may inhibit multiple biological pathways to control biofilm formation. 相似文献
997.
Dhouha Bohli-Abderrazek Raja Jelassi Elfed Morgan Karima Nasri-Ammar 《Biological Rhythm Research》2017,48(4):607-621
The locomotor activity rhythm of the sandhopper Talitrus saltator (Amphipoda Talitridae) was investigated in Madfoun beach. The rhythm was monitored in individual and group animals during 21 days at constant temperature. During the first two weeks, animals were kept under light–dark cycle (d1–d7) and constant darkness (d8–d14). Light pulses of 2 h were applied, at the end of the experimental night, during the first 3 days of the third week (d15–d18). Then, constant darkness was restored for the rest of the experiment (d19–d21). Results revealed that Talitrus saltator individuals as well as groups concentrated their activities in experimental night under light–dark cycle and in the presence of pulses; whereas, a clear drift of activity is observed under constant darkness. Periodogram analysis showed the presence of circadian component whatever the recording type. An ultradian period was revealed in individual recording whatever the regimen, while for groups, this component appeared only under nLD cycle. Furthermore, the locomotor rhythm is more defined under nLD cycle for individuals and in constant darkness for groups. 相似文献
998.
Anas Ayari Raja Jelassi Chedlia Ghemari Karima Nasri-Ammar 《Biological Rhythm Research》2017,48(3):449-457
Locomotor activity rhythm of fresh adult of H. reaumurii was recorded in pairs with ovigerous and with non-ovigerous females. According to double-plotted actograms and waveform curves, results showed the presence of different locomotor patterns. In fact, locomotor profiles of pairs with ovigerous females were mainly bimodal whatever the recording conditions, whereas locomotor patterns were trimodal in pairs with non-ovigerous females. Results showed also that locomotor activity rhythm was more stable in the presence of the synchronizer (nLD cycle) than in constant darkness whatever the recording type. Moreover, the most important stability of the locomotor rhythm was observed under constant darkness and individuals were more active in pairs with ovigerous females than in pairs with non-ovigerous females. 相似文献
999.
Amantullah Ansari Sharad Satalkar Varshavekumar Patil Amit S. Shete Simranjeet Kaur Ashu Gupta Siddhartha Singh Mohd. Raja Daniel L. Severance Sebastián Bernales Sarvajit Chakravarty David T. Hung Son M. Pham Francisco J. Herrera Roopa Rai 《Bioorganic & medicinal chemistry letters》2017,27(2):217-222
EZH2 (enhancer of zeste homologue 2) is the catalytic subunit of the polycomb repressive complex 2 (PRC2) that catalyzes the methylation of lysine 27 of histone H3 (H3K27). Dysregulation of EZH2 activity is associated with several human cancers and therefore EZH2 inhibition has emerged as a promising therapeutic target. Several small molecule EZH2 inhibitors with different chemotypes have been reported in the literature, many of which use a bicyclic heteroaryl core. Herein, we report the design and synthesis of EZH2 inhibitors containing an indoline core. Partial saturation of an indole to an indoline provided lead compounds with nanomolar activity against EZH2, while also improving solubility and oxidative metabolic stability. 相似文献
1000.
Mindfulness‐Based Stress Reduction in Women with Overweight or Obesity: A Randomized Clinical Trial
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