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Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites
, 2000
"... Motivation: In order to extract protein sequences from nucleotide sequences, it is an important step to recognize points at which regions start that code for proteins. These points are called translation initiation sites (TIS). Results: The task of finding TIS can be modeled as a classification pro ..."
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Cited by 131 (14 self)
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Motivation: In order to extract protein sequences from nucleotide sequences, it is an important step to recognize points at which regions start that code for proteins. These points are called translation initiation sites (TIS). Results: The task of finding TIS can be modeled as a classification problem. We demonstrate the applicability of support vector machines (SVMs) for this task, and show how to incorporate prior biological knowledge by engineering an appropriate kernel function. With the described techniques the recognition performance can be improved by 26% over leading existing approaches. We provide evidence that existing related methods (e.g. ESTScan) could profit from advanced TIS recognition.
Translation of human hepatitis C virus RNA in cultured cells is mediated by an internal ribosome-binding mechanism
- J. Virol
, 1993
"... The human hepatitis C virus (HCV) contains a long 5 ' noncoding region (5 ' NCR). Computer-assisted and biochemical analyses suggest that there is a complex secondary structure in this region that is comparable to the secondary structures that are found in picornaviruses (E. A. Brown, H. Z ..."
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Cited by 106 (3 self)
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The human hepatitis C virus (HCV) contains a long 5 ' noncoding region (5 ' NCR). Computer-assisted and biochemical analyses suggest that there is a complex secondary structure in this region that is comparable to the secondary structures that are found in picornaviruses (E. A. Brown, H. Zhang, L.-H. Ping, and S. M. Lemon, Nucleic Acids Res. 20:5041-5045, 1992). Previous in vitro studies suggest that the HCV 5 ' NCR plays an important role during translation (K. Tsukiyama-Kohara, N. lizuka, M. Kohara, and A. Nomoto, J. Virol. 66:1476-1483, 1992). Dicistronic and monocistronic expression vectors, in vitro translation, RNA transfec-tions, and deletion mutagenesis studies were utilized to demonstrate unambiguously that the HCV 5 ' NCR is involved in translational control. Our data strongly support the conclusion that an internal ribosome entry site exists within the 5 ' noncoding sequences proximal to the initiator AUG. Furthermore, our results suggest that the HCV genome is translated in a cap-independent manner and that the sequences immediately upstream of the initiator AUG are essential for internal ribosome entry site function during translation. Hepatitis C virus (HCV) is the documented etiologic agent of blood-borne non-A, non-B hepatitis and represents the principal infectious agent associated with posttransfusion hepatitis (4). Recent clinical studies have demonstrated a strong correlation between HCV infection and hepatocellu-lar carcinoma (28). The HCV genome is a single-stranded RNA molecule with plus-strand polarity and is approxi-mately 9,500 nucleotides (nt) long (5, 13, 18, 24, 32). On the basis of sequence comparisons and in vitro translation studies, the HCV genome appears to encode several struc-tural and nonstructural proteins (Fig. 1) (4, 12, 23). This information, in conjunction with additional characteristics, has led to the tentative classification of HCV in the family
Canonical eukaryotic initiation factors determine initiation of translation by internal ribosomal entry
- Mol. Cell Biol
, 1996
"... Translation of picornavirus RNA is initiated after ribosomal binding to an internal ribosomal entry site (IRES) within the 5 * untranslated region.We have reconstituted IRES-mediated initiation on encephalomyocar-ditis virus RNA from purified components and used primer extension analysis to confirm ..."
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Cited by 103 (23 self)
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Translation of picornavirus RNA is initiated after ribosomal binding to an internal ribosomal entry site (IRES) within the 5 * untranslated region.We have reconstituted IRES-mediated initiation on encephalomyocar-ditis virus RNA from purified components and used primer extension analysis to confirm the fidelity of 48S pre-initiation complex formation. Eukaryotic initiation factor 2 (eIF2), eIF3, and eIF4F were required for initiation; eIF4B and to a lesser extent the pyrimidine tract-binding protein stimulated this process. We show that eIF4F binds to the IRES in a novel cap-independent manner and suggest that cap- and IRES-dependent initiation mechanisms utilize different modes of interaction with this factor to promote ribosomal attachment to mRNA. Initiation of eukaryotic protein synthesis is the process of assembly of an 80S initiation complex containing initiator tRNAi Met, 40S, and 60S ribosomal subunits at the initiation codon of an mRNA (42). The first step in this process is formation of a 43S complex that consists of eukaryotic initia-tion factor 2 (eIF2), eIF3, and initiator Met-tRNAi Met bound to
Functional dissociation of paracellular permeability and transepithelial electrical resistance and disruption of the apical-basolateral intramembrane diffusion barrier by expression of a mutant tight junction membrane protein
, 1996
"... Abstract. Tight junctions, the most apical of the intercellular junctions that connect individual cells in a epithelial sheet, are thought to form a seal that restricts paracellular and intramembrane diffusion. To analyze the functioning of tight junctions, we generated stable MDCK strain 2 cell lin ..."
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Cited by 86 (9 self)
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Abstract. Tight junctions, the most apical of the intercellular junctions that connect individual cells in a epithelial sheet, are thought to form a seal that restricts paracellular and intramembrane diffusion. To analyze the functioning of tight junctions, we generated stable MDCK strain 2 cell lines expressing either full-length or COOH-terminally truncated chicken occludin, the only known transmembrane component of tight junctions. Confocal immunofluorescence and immunoelectron microscopy demonstrated that mutant occludin was incorporated into tight junctions but, in contrast to full-length chicken occludin, exhibited a discontinuous junctional staining pattern and also disrupted the continuous junctional ring formed by endogenous occludin. This rearrangement of occludin was not paralleled by
Neural Network Prediction of Translation Initiation Sites in Eukaryotes: Perspectives for EST and Genome analysis
- In ISMB’97
, 1997
"... Translation in eukaryotes does not always start at the first AUG in an mRNA, implying that context information also plays a role. This makes prediction of translation initiation sites a non-trivial task, especially when analysing EST and genome data where the entire mature mRNA sequence is not known ..."
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Cited by 74 (1 self)
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Translation in eukaryotes does not always start at the first AUG in an mRNA, implying that context information also plays a role. This makes prediction of translation initiation sites a non-trivial task, especially when analysing EST and genome data where the entire mature mRNA sequence is not known. In this paper, we employ artificial neural networks to predict which AUG triplet in an mRNA sequence is the start codon. The trained networks correctly classified 88 % of Arabidopsis and 85 % of vertebrate AUG triplets. We find that our trained neural networks use a combination of local start eodon context and global sequence information. Furthermore, analysis of false predictions shows that AUGs in frame with the actual start codon are more frequently selected than out-of-frame AUGs, suggesting that our networks use reading frame detection. A number of conflicts between neural network predictions and database annotations are analysed in detail, leading to identification of possible database errors.
Occludin: a novel integral membrane protein localizing at tight junctions
- 1777 – 1788
, 1993
"... Abstract. Recently, we found that ZO-1, a tight junction-associated protein, was concentrated in the so called isolated adherens junction fraction from the ..."
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Cited by 68 (1 self)
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Abstract. Recently, we found that ZO-1, a tight junction-associated protein, was concentrated in the so called isolated adherens junction fraction from the
Molecular characterization and tissue distribution of ZO-2, a tight junction protein homologous to ZO-1 and the Drosophila discs-large tumor suppressor protein
- J. Cell
, 1994
"... Abstract. ZO-1 is a 210-225-kD peripheral membrane protein associated with cytoplasmic surfaces of the zonula occludens or tight junction. A 160-kD polypeptide, designated ZO-2, was found to coimmunoprecipitate with ZO-1 from MDCK cell extracts prepared under conditions which preserve protein associ ..."
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Cited by 64 (3 self)
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Abstract. ZO-1 is a 210-225-kD peripheral membrane protein associated with cytoplasmic surfaces of the zonula occludens or tight junction. A 160-kD polypeptide, designated ZO-2, was found to coimmunoprecipitate with ZO-1 from MDCK cell extracts prepared under conditions which preserve protein associations
Synaptopodin: An Actin-associated Protein in Telencephalic Dendrites
"... Abstract. Synaptopodin is an actin-associated protein of differentiated podocytes that also occurs as part of the actin cytoskeleton of postsynaptic densities (PSD) and associated dendritic spines in a subpopulation of exclusively telencephalic synapses. Amino acid sequences determined in purified r ..."
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Cited by 59 (7 self)
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Abstract. Synaptopodin is an actin-associated protein of differentiated podocytes that also occurs as part of the actin cytoskeleton of postsynaptic densities (PSD) and associated dendritic spines in a subpopulation of exclusively telencephalic synapses. Amino acid sequences determined in purified rat kidney and forebrain synaptopodin and derived from human and mouse brain cDNA clones show no significant homology to any known protein. In particular, synaptopodin does not contain functional domains found in receptor-clustering PSD proteins. The open reading frame of synaptopodin encodes a polypeptide with a calculated M r of 73.7 kD (human)/74.0 kD (mouse) and an isoelectric point of 9.38 (human)/9.27 (mouse). Synaptopodin contains a high amount of proline (�20%) equally distributed
Cdc42 regulates anchorage-independent growth and is necessary for Ras transformation. Mol Cell Biol 17: 3449–3458
, 1997
"... Cdc42 regulates anchorage-independent growth and is necessary for Ras transformation. ..."
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Cited by 46 (1 self)
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Cdc42 regulates anchorage-independent growth and is necessary for Ras transformation.
The human immunodeficiency virus type 1 gag gene encodes an internal ribosome entry site
- J
, 2001
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