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Background
The mRNA translation initiation region (TIR) comprises the initiator codon, Shine-Dalgarno (SD) sequence and translational enhancers. Probably the most abundant class of enhancers contains A/U-rich sequences. We have tested the influence of SD sequence length and the presence of enhancers on the efficiency of translation initiation. 相似文献2.
Background
Algorithmic approaches to splice site prediction have relied mainly on the consensus patterns found at the boundaries between protein coding and non-coding regions. However exonic splicing enhancers have been shown to enhance the utilization of nearby splice sites. 相似文献3.
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Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in <Emphasis Type="Italic">Drosophila melanogaster</Emphasis> and <Emphasis Type="Italic">Drosophila pseudoobscura</Emphasis>
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Berman BP Pfeiffer BD Laverty TR Salzberg SL Rubin GM Eisen MB Celniker SE 《Genome biology》2004,5(9):R61
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Background
Recent genomic scale survey of epigenetic states in the mammalian genomes has shown that promoters and enhancers are correlated with distinct chromatin signatures, providing a pragmatic way for systematic mapping of these regulatory elements in the genome. With rapid accumulation of chromatin modification profiles in the genome of various organisms and cell types, this chromatin based approach promises to uncover many new regulatory elements, but computational methods to effectively extract information from these datasets are still limited. 相似文献7.
Jennifer M Reynolds Kamal El Bissati Jens Brandenburg Arthur Günzl Choukri Ben Mamoun 《BMC clinical pharmacology》2007,7(1):13
Background
The high rate of mortality due to malaria and the worldwide distribution of parasite resistance to the commonly used antimalarial drugs chloroquine and pyrimethamine emphasize the urgent need for the development of new antimalarial drugs. An alternative approach to the long and uncertain process of designing and developing new compounds is to identify among the armamentarium of drugs already approved for clinical treatment of various human diseases those that may have strong antimalarial activity. 相似文献8.
Doris Hartinger Stefan Heinl Heidi Elisabeth Schwartz Reingard Grabherr Gerd Schatzmayr Dietmar Haltrich Wulf-Dieter Moll 《Microbial cell factories》2010,9(1):62
Background
Fumonisin B1 is a cancerogenic mycotoxin produced by Fusarium verticillioides and other fungi. Sphingopyxis sp. MTA144 can degrade fumonisin B1, and a key enzyme in the catabolic pathway is an aminotransferase which removes the C2-amino group from hydrolyzed fumonisin B1. In order to study this aminotransferase with respect to a possible future application in enzymatic fumonisin detoxification, we attempted expression of the corresponding fumI gene in E. coli and purification of the enzyme. Since the aminotransferase initially accumulated in inclusion bodies, we compared the effects of induction level, host strain, expression temperature, solubility enhancers and a fusion partner on enzyme solubility and activity. 相似文献9.
Background
Laccases are multi-copper oxidases that catalyze the one electron oxidation of a broad range of compounds. Laccase substrates include substituted phenols, arylamines and aromatic thiols. Such compounds are activated by the enzyme to the corresponding radicals. Owing to their broad substrate range laccases are considered to be versatile biocatalysts which are capable of oxidizing natural and non-natural industrial compounds, with water as sole by-product. 相似文献10.
Wojciech Filipiak Andreas Sponring Tomas Mikoviny Clemens Ager Jochen Schubert Wolfram Miekisch Anton Amann Jakob Troppmair 《Cancer cell international》2008,8(1):17
Background
The aim of this work was to confirm the existence of volatile organic compounds (VOCs) specifically released or consumed by lung cancer cells. 相似文献11.
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Miglena Koprinarova Petya Markovska Ivan Iliev Boyka Anachkova George Russev 《BMC molecular biology》2010,11(1):49
Background
Histone deacetylase inhibitors have been proposed as potential enhancers of the cytotoxic effect of cisplatin and other anticancer drugs. Their application would permit the use of lower therapeutic doses and reduction of the adverse side effects of the drugs. However, the molecular mechanisms by which they sensitize the cells towards anticancer drugs are not known in details, which is an obstacle in developing effective therapeutic protocols. 相似文献13.
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Background
Sulphur compounds like cysteine, methionine and S-adenosylmethionine are essential for the viability of most cells. Thus many organisms have developed a complex regulatory circuit that governs the expression of enzymes involved in sulphur assimilation and metabolism. In the filamentous fungus Hypocrea jecorina (anamorph Trichoderma reesei) little is known about the participants in this circuit. 相似文献15.
Min Xu Zeng Wanwen Chen Shengquan Chen Ning Chen Ting Jiang Rui 《BMC bioinformatics》2017,18(13):478-46
Background
With the rapid development of deep sequencing techniques in the recent years, enhancers have been systematically identified in such projects as FANTOM and ENCODE, forming genome-wide landscapes in a series of human cell lines. Nevertheless, experimental approaches are still costly and time consuming for large scale identification of enhancers across a variety of tissues under different disease status, making computational identification of enhancers indispensable.Results
To facilitate the identification of enhancers, we propose a computational framework, named DeepEnhancer, to distinguish enhancers from background genomic sequences. Our method purely relies on DNA sequences to predict enhancers in an end-to-end manner by using a deep convolutional neural network (CNN). We train our deep learning model on permissive enhancers and then adopt a transfer learning strategy to fine-tune the model on enhancers specific to a cell line. Results demonstrate the effectiveness and efficiency of our method in the classification of enhancers against random sequences, exhibiting advantages of deep learning over traditional sequence-based classifiers. We then construct a variety of neural networks with different architectures and show the usefulness of such techniques as max-pooling and batch normalization in our method. To gain the interpretability of our approach, we further visualize convolutional kernels as sequence logos and successfully identify similar motifs in the JASPAR database.Conclusions
DeepEnhancer enables the identification of novel enhancers using only DNA sequences via a highly accurate deep learning model. The proposed computational framework can also be applied to similar problems, thereby prompting the use of machine learning methods in life sciences.16.
Vishaldeep K Sidhu Frank-Jörg Vorhölter Karsten Niehaus Steven A Watt 《BMC microbiology》2008,8(1):87
Background
Outer membrane vesicles (OMVs) are released from the outer membrane of many Gram-negative bacteria. These extracellular compartments are known to transport compounds involved in cell-cell signalling as well as virulence associated proteins, e.g. the cytolysine from enterotoxic E. coli. 相似文献17.
Diane M Ramos Firdous Kamal Ernst A Wimmer Alexander N Cartwright Antónia Monteiro 《BMC developmental biology》2006,6(1):55-7
Background
Precise temporal and spatial regulation of transgene expression is a critical tool to investigate gene function in developing organisms. The most commonly used technique to achieve tight control of transgene expression, however, requires the use of specific DNA enhancers that are difficult to characterize in non-model organisms. Here, we sought to eliminate the need for this type of sequence-based gene regulation and to open the field of functional genetics to a broader range of organisms. 相似文献18.
Background
Older adults with cognitive problems have a higher risk of falls, at least twice that of cognitively normal older adults. The consequences of falls in this population are very serious: fallers with cognitive problems suffer more injuries due to falls and are approximately five times more likely to be admitted to institutional care. Although the mechanisms of increased fall risk in cognitively impaired people are not completely understood, it is known that impaired cognitive abilities can reduce attentional resource allocation while walking. Since cognitive enhancers, such as cholinesterase inhibitors, improve attention and executive function, we hypothesise that cognitive enhancers may reduce fall risk in elderly people in the early stages of cognitive decline by improving their gait and balance performance due to an enhancement in attention and executive function. 相似文献19.
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