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Relevant bibliographies by topics / Translation initiation sites

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Academic literature on the topic 'Translation initiation sites'

Author: Grafiati

Published: 4 June 2021

Last updated: 18 February 2022

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Journal articles on the topic "Translation initiation sites"

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Paek, Ki Young, Ka Young Hong, Incheol Ryu, Sung Mi Park, Sun Ju Keum, Oh Sung Kwon, and Sung Key Jang. "Translation initiation mediated by RNA looping." Proceedings of the National Academy of Sciences 112, no. 4 (January 12, 2015): 1041–46. http://dx.doi.org/10.1073/pnas.1416883112.

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Eukaryotic translation initiation commences at the initiation codon near the 5′ end of mRNA by a 40S ribosomal subunit, and the recruitment of a 40S ribosome to an mRNA is facilitated by translation initiation factors interacting with the m7G cap and/or poly(A) tail. The 40S ribosome recruited to an mRNA is then transferred to the AUG initiation codon with the help of translation initiation factors. To understand the mechanism by which the ribosome finds an initiation codon, we investigated the role of eIF4G in finding the translational initiation codon. An artificial polypeptide eIF4G fused with MS2 was localized downstream of the reporter gene through MS2-binding sites inserted in the 3′ UTR of the mRNA. Translation of the reporter was greatly enhanced by the eIF4G-MS2 fusion protein regardless of the presence of a cap structure. Moreover, eIF4G-MS2 tethered at the 3′ UTR enhanced translation of the second cistron of a dicistronic mRNA. The encephalomyocarditis virus internal ribosome entry site, a natural translational-enhancing element facilitating translation through an interaction with eIF4G, positioned downstream of a reporter gene, also enhanced translation of the upstream gene in a cap-independent manner. Finally, we mathematically modeled the effect of distance between the cap structure and initiation codon on the translation efficiency of mRNAs. The most plausible explanation for translational enhancement by the translational-enhancing sites is recognition of the initiation codon by the ribosome bound to the ribosome-recruiting sites through “RNA looping.” The RNA looping hypothesis provides a logical explanation for augmentation of translation by enhancing elements located upstream and/or downstream of a protein-coding region.

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Gelsinger, Diego Rivera, Emma Dallon, Rahul Reddy, Fuad Mohammad, Allen R. Buskirk, and Jocelyne DiRuggiero. "Ribosome profiling in archaea reveals leaderless translation, novel translational initiation sites, and ribosome pausing at single codon resolution." Nucleic Acids Research 48, no. 10 (May 8, 2020): 5201–16. http://dx.doi.org/10.1093/nar/gkaa304.

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Abstract High-throughput methods, such as ribosome profiling, have revealed the complexity of translation regulation in Bacteria and Eukarya with large-scale effects on cellular functions. In contrast, the translational landscape in Archaea remains mostly unexplored. Here, we developed ribosome profiling in a model archaeon, Haloferax volcanii, elucidating, for the first time, the translational landscape of a representative of the third domain of life. We determined the ribosome footprint of H. volcanii to be comparable in size to that of the Eukarya. We linked footprint lengths to initiating and elongating states of the ribosome on leadered transcripts, operons, and on leaderless transcripts, the latter representing 70% of H. volcanii transcriptome. We manipulated ribosome activity with translation inhibitors to reveal ribosome pausing at specific codons. Lastly, we found that the drug harringtonine arrested ribosomes at initiation sites in this archaeon. This drug treatment allowed us to confirm known translation initiation sites and also reveal putative novel initiation sites in intergenic regions and within genes. Ribosome profiling revealed an uncharacterized complexity of translation in this archaeon with bacteria-like, eukarya-like, and potentially novel translation mechanisms. These mechanisms are likely to be functionally essential and to contribute to an expanded proteome with regulatory roles in gene expression.

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Ganoza, M. C., E. C. Kofoid, P. Marlière, and B. G. Louis. "Potential secondary structure at translation-initiation sites." Nucleic Acids Research 16, no. 9 (1988): 4196. http://dx.doi.org/10.1093/nar/16.9.4196-a.

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Ganoza, M. C., E. C. Kofoid, P. Marlière, and B. G. Louis. "Potential secondary structure at translation-initiation sites." Nucleic Acids Research 15, no. 1 (1987): 345–60. http://dx.doi.org/10.1093/nar/15.1.345.

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Robbins-Pianka, A., M. D. Rice, and M. P. Weir. "The mRNA landscape at yeast translation initiation sites." Bioinformatics 26, no. 21 (September 6, 2010): 2651–55. http://dx.doi.org/10.1093/bioinformatics/btq509.

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Zhang, Sai, Hailin Hu, Tao Jiang, Lei Zhang, and Jianyang Zeng. "TITER: predicting translation initiation sites by deep learning." Bioinformatics 33, no. 14 (July 12, 2017): i234—i242. http://dx.doi.org/10.1093/bioinformatics/btx247.

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Choi, Myoung-Kwon, Sung-Dong Park, In-Sick Park, and Il-Soo Moon. "Localization of Translation Initiation Factors to the Postsynaptic Sites." Journal of Life Science 21, no. 11 (November 30, 2011): 1526–31. http://dx.doi.org/10.5352/jls.2011.21.11.1526.

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Li, Guo-Liang, and Tze-Yun Leong. "Feature Selection for the Prediction of Translation Initiation Sites." Genomics, Proteomics & Bioinformatics 3, no. 2 (2005): 73–83. http://dx.doi.org/10.1016/s1672-0229(05)03012-3.

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Sendoel, Ataman, Joshua G. Dunn, Edwin H. Rodriguez, Shruti Naik, Nicholas C. Gomez, Brian Hurwitz, John Levorse, et al. "Translation from unconventional 5′ start sites drives tumour initiation." Nature 541, no. 7638 (January 2017): 494–99. http://dx.doi.org/10.1038/nature21036.

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Shah, O. Jameel, Joshua C. Anthony, Scot R. Kimball, and Leonard S. Jefferson. "4E-BP1 and S6K1: translational integration sites for nutritional and hormonal information in muscle." American Journal of Physiology-Endocrinology and Metabolism 279, no. 4 (October 1, 2000): E715—E729. http://dx.doi.org/10.1152/ajpendo.2000.279.4.e715.

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Maintenance of cellular protein stores in skeletal muscle depends on a tightly regulated synthesis-degradation equilibrium that is conditionally modulated under an extensive range of physiological and pathophysiological circumstances. Recent studies have established the initiation phase of mRNA translation as a pivotal site of regulation for global rates of protein synthesis, as well as a site through which the synthesis of specific proteins is controlled. The protein synthetic pathway is exquisitely sensitive to the availability of hormones and nutrients and employs a comprehensive integrative strategy to interpret the information provided by hormonal and nutritional cues. The translational repressor, eukaryotic initiation factor 4E binding protein 1 (4E-BP1), and the 70-kDa ribosomal protein S6 kinase (S6K1) have emerged as important components of this strategy, and together they coordinate the behavior of both eukaryotic initiation factors and the ribosome. This review discusses the role of 4E-BP1 and S6K1 in translational control and outlines the mechanisms through which hormones and nutrients effect changes in mRNA translation through the influence of these translational effectors.

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Dissertations / Theses on the topic "Translation initiation sites"

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Booden, Helen C. "Translation initiation factor requirements of the cyclinT1 and set7 apoptotic internal ribosome entry sites." Thesis, University of Nottingham, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.523033.

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Steimer, Sarah Reath. "Investigation of novel ribosomal recognition sites in Escherichia coli noncanonical mRNAs containing multiple start codons." Miami University / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=miami1461847705.

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Berg, Emily Katherine. "Thermodynamics of λ-PCR Primer Design and Effective Ribosome Binding Sites." Thesis, Virginia Tech, 2019. http://hdl.handle.net/10919/89900.

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Recombinant DNA technology has been commonly used in a number of fields to synthesize new products or generate products with a new pathway. Conventional cloning methods are expensive and require significant time and labor; λ-PCR, a new cloning method developed in the Senger lab, has a number of advantages compared to other cloning processes due to its employment of relatively inexpensive and widely available materials and time-efficiency. While the amount of lab work required for the cloning process is minimal, the importance of accurate primer design cannot be overstated. The target of this study was to create an effective procedure for λ-PCR primer design that ensures accurate cloning reactions. Additionally, synthetic ribosome binding sites (RBS) were included in the primer designs to test heterologous protein expression of the cyan fluorescent reporter with different RBS strengths. These RBS sequences were designed with an online tool, the RBS Calculator. A chimeric primer design procedure for λ-PCR was developed and shown to effectively create primers used for accurate cloning with λ-PCR; this method was used to design primers for CFP cloning in addition to two enzymes cloned in the Senger lab. A total of five strains of BL21(DE3) with pET28a + CFP were constructed, each with the same cyan fluorescent protein (CFP) reporter but different RBS sequences located directly upstream of the start codon of the CFP gene. Expression of the protein was measured using both whole-cell and cell-free systems to determine which system yields higher protein concentrations. A number of other factors were tested to optimize conditions for high protein expression, including: induction time, IPTG concentration, temperature, and media (for the cell-free experiments only). Additionally, expression for each synthetic RBS sequence was investigated to determine an accurate method for predicting protein translation. NUPACK and the Salis Lab RBS Calculator were both used to evaluate the effects of these different synthetic RBS sequences. The results of the plate reader experiments with the 5 CFP strains revealed a number of factors to be statistically significant when predicting protein expression, including: IPTG concentration, induction time, and in the cell-free experiments, type of media. The whole-cell system consistently produced higher amounts of protein than the cell-free system. Lastly, contrasts between the CFP strains showed each strain's performance did not match the predictions from the RBS Calculator. Consequently, a new method for improving protein expression with synthetic RBS sequences was developed using relationships between Gibbs free energy of the RBS-rRNA complex and expression levels obtained through experimentation. Additionally, secondary structure present at the RBS in the mRNA transcript was modeled with strain expression since these structures cause deviations in the relationship between Gibbs free energy of the mRNA-rRNA complex and CFP expression.
Master of Science
Recombinant DNA technology has been used to genetically enhance organisms to produce greater amounts of a product already made by the organism or to make an organism synthesize a new product. Genes are commonly modified in organisms using cloning practices which typically involves inserting a target gene into a plasmid and transforming the plasmid into the organism of interest. A new cloning process developed in the Senger lab, λ-PCR, improves the cloning process compared to other methods due to its use of relatively inexpensive materials and high efficiency. A primary goal of this study was to develop a procedure for λ-PCR primer design that allows for accurate use of the cloning method. Additionally, this study investigated the use of synthetic ribosome binding sites to control and improve expression of proteins cloned into an organism. Ribosome binding sites are sequences located upstream of the gene that increase the molecule’s affinity for the rRNA sequence on the ribosome, bind to the ribosome just upstream of the beginning of the gene, and initiate expression of the gene. Tools have been developed that create synthetic ribosome binding sites designed to produce specific amounts of protein. For example, the tools can increase or decrease expression of a gene depending on the application. These tools, the Salis Lab RBS Calculator and NUPACK, were used to design and evaluate the effects of the synthetic ribosome binding sites. Additionally, a new method was created to design synthetic ribosome binding sites since the methods used during the design process yielded inaccuracies. Each strain of E. coli contained the same gene, a cyan fluorescent protein (CFP), but had different RBS sequences located upstream of the gene. Expression of CFP was controlled via induction, meaning the addition of a particular molecule, IPTG in this system, triggered expression of CFP. Each of the CFP strains were tested with a variety of v conditions in order to find the conditions most suitable for protein expression; the variables tested include: induction time, IPTG (inducer) concentration, and temperature. Media was also tested for the cell-free systems, meaning the strains were grown overnight for 18 hours and lysed, a process where the cell membrane is broken in order to utilize the cell’s components for protein expression; the cell lysate was resuspended in new media for the experiments. ANOVA and multiple linear regression revealed IPTG concentration, induction time, and media to be significant factors impacting protein expression. This analysis also showed each CFP strain did not perform as the RBS Calculator predicted. Modeling each strain’s CFP expression using the RBS-rRNA binding strengths and secondary structures present in the RBS allowed for the creation of a new model for predicting and designing RBS sequences.

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Qin, Daoming. "Role of 16S Ribosomal RNA in Translation Initiation." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1299007063.

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Croitoru, Victor. "Study on the Function of Translation Initiation Factor IF1." Doctoral thesis, Stockholm : Department of Genetics, Microbiology and Toxicology, Stockholm University, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-1032.

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Sadahiro, Akitoshi. "Translation of Hepatitis A Virus IRES Is Upregulated by a Hepatic Cell-Specific Factor." Kyoto University, 2019. http://hdl.handle.net/2433/242387.

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Takyar, Seyedtaghi. "Translation initiation in HCV : the effect of cyanocobalamin on the structure and function of the HCV internal ribosomal entry site /." St. Lucia, Qld, 2001. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe17570.pdf.

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Mengardi, Chloé. "Étude de l'effet des microARN sur l'initiation de la traduction dirigée par l'IRES du Virus de l'Hépatite C." Thesis, Lyon, 2016. http://www.theses.fr/2016LYSEN001.

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Les microARN (miARN) sont de petits ARN non-codants qui contrôlent l’expression génique, en s’hybridant, le plus souvent, de manière imparfaite à des séquences spécifiques qui se trouvent généralement dans la région non traduite en 3' (3’UTR) de transcrits cibles. Les miARN guident sur l’ARN messager (ARNm) un complexe protéique appelé RNA-induced Silencing Complex (RISC), composé des protéines Argonaute et TNRC6, qui perturbe l’initiation de la traduction et provoque la déadénylation et la dégradation du transcrit. C'est l’interaction entre le RISC et le complexe de pré-initiation de la traduction 43S (composé de la petite sous-unité ribosomique 40S et des facteurs d’initiation associés) qui entraîne la répression traductionnelle de l’ARNm ciblé. Des résultats récents ont démontré que le RISC perturbe le balayage de la région non traduite en 5’ (5’UTR) par le ribosome, étape qui requiert la présence de 2 facteurs d’initiation qui sont eIF4F qui reconnaît et lie la coiffe ainsi que la protéine PABP, fixée le long de la queue poly(A). Toutefois, les miARN peuvent également induire la stimulation de la traduction des transcrits cibles dans les cellules quiescentes, dans un lysat d’embryons de drosophiles ou encore dans les ovocytes de Xénope. Le mécanisme moléculaire de stimulation de l’expression par les miARN est encore mal connu mais requiert l’absence de queue poly(A) en 3’ des ARN cible et de TNRC6 au sein du complexe RISC. Le Virus de l’Hépatite C (VHC) possède en 5’ de son ARNg un site d’entrée interne du ribosome (IRES) qui recrute la petite sous-unité ribosomique 40S, sans nécessiter la reconnaissance de la coiffe par eIF4F, ni la protéine PABP, ni le balayage de la 5’UTR par le ribosome. Ces caractéristiques singulières nous ont conduits à rechercher l'impact du complexe RISC fixé en 3’ de l’ARNm sur l’initiation de la traduction du VHC. Pour cela, nous avons utilisé des transcrits contenant l'IRES du VHC en 5' et des sites d’hybridation du miARN let-7 en 3’. Ces ARNm ont ensuite été transfectés dans des lignées cellulaires hépatocytaires, ou non. A notre grande surprise, nous avons observé que la fixation du miARN let-7 sur la région 3' du transcrit stimulait fortement l’expression dirigée par l’IRES de VHC. Toutefois, l’augmentation de l’expression n’est pas due à la stabilisation du transcrit mais bien à une hausse significative de la synthèse protéique indépendamment d’un quelconque effet de miR-122. En utilisant d’autres IRES dites 'HCV-like', nous avons pu confirmer ces résultats et démontrer que, l’ajout d’une queue poly(A) en 3’ du transcrit, capable de fixer la PABP, annule cet effet stimulateur suggérant que l’absence de cette protéine est nécessaire pour que le complexe RISC stimule la traduction du VHC
MicroRNAs (miRNAs) are small non coding RNAs which control gene expression by recognizing and hybridizing to a specific sequence generally located in the 3’UTR of targeted messenger RNA (mRNA). miRNAs serve as a guide for the RNA-Induced Silencing Complex (RISC) that is composed by, at least, the Argonaute proteins and TNRC6. Recent studies have suggested that translation inhibition occurs first and is then followed by deadenylation and degradation of the targeted transcript. The miRNA-induced inhibition of protein synthesis occurs at the level of translation initiation during the ribosomal scanning step and it requires the presence of both the initiation factor eIF4G and the poly(A) Binding Protein (PABP). In this process, the RISC interacts with both PABP and 43S pre-initiation complex (composed by initiation factors and ribosome) and it results in the disruption of linear scanning of the ribosome along the 5’ Untranslated Region (5’UTR). In some specific cases, the binding of miRNAs to their target sequences can upregulate translation initiation. This has notably been demonstrated in G0 quiescent cells, drosophila embryos and Xenopus oocytes. Although the molecular mechanism by which upregulation occurs remains to be precisely determined, it appears that the absence of a poly(A) tail and the lack of availability of the TNRC6 proteins are amongst the major determinants. In the particular case of the Hepatitis C Virus (HCV), the genomic RNA is uncapped and non polyadenylated and harbors an Internal Ribosome Entry Site (IRES) which directly binds to the ribosome with no need for cap-recognition, PABP binding and ribosome scanning. These peculiar features of the HCV IRES prompted us to investigate how viral translation can be regulated by the miRNA machinery. In order to do that, we have used a mRNA that contains the HCV IRES in 5’ and 4 let-7 binding sites in its 3’ extremity. To most of our surprise, we have observed a strong stimulation of the expression of the HCV IRES when the construct is bearing the let-7 sites. This effect is not due to any interference with the miR-122 binding sites although the magnitude of stimulation reached the same level. Our data show that it is the presence of the RISC on the 3' end of the transcript that can stimulate internal ribosome entry at the 5' end. By using other HCV-like IRESes, we could confirm these data and further showed that the absence of a poly(A) tail was an absolute requirement for the stimulation to occur. These effects are not due to an increase of mRNA stability and are rather exerted at the level of translation

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Zhang, Yuanyuan. "TRANSLATIONAL REGULATORY MECHANISMS OF THE RAT AND HUMAN MULTIDRUG RESISTANCE PROTEIN 2." UKnowledge, 2008. http://uknowledge.uky.edu/gradschool_diss/649.

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Multidrug resistance protein 2 (MRP2) is the second member the C subfamily in the superfamily of adenosine triphosphate (ATP)-binding cassette (ABC) efflux transporters. MRP2 is a critical player for generation of bile acidindependent bile flow and biliary excretion of glutathione, glucuronate and sulfate conjugates of endo- and xenobiotics. Dysfunctional expression of MRP2 is associated with Dubin-Johnson Syndrome. Pathological and physiological states or xenobiotics change the MRP2 expression level. Under some conditions, expression of the human MRP2 and rat Mrp2 proteins are regulated at the translation level. There are several transcription initiation sites in MRP2/Mrp2 gene. The 5’ untranslated regions (5’UTRs) of MRP2/Mrp2 contains multiple translation start codons. The focus of this study, therefore, was investigation of the translational regulatory mechanisms mediated by the upstream open reading frames (uORF) of MRP2/Mrp2. Using in vitro translation assays and transient cotransfection assays in HepG2 cells, we showed that the rat uORF1 starting at position -109 (relative to the ATG of Mrp2) and the human uORF2 starting at position -105 (relative to the ATG of MRP2) are two major cis-acting inhibitors of translation among the rat and human multiple uORFs, respectively. Translational regulation mediated by the uORFs in the rat Mrp2 mRNA is a combined effect of the leaky scanning model and the reinitiation model, and also results from interaction of the multiple uORFs. In addition, by Ribonuclease Protection Assays (RPA), we detected multiple transcription initiation sites of MRP2/Mrp2 gene in tissues. We also found that the relative abundance of the rat Mrp2 mRNA isoforms with different 5’UTRs differed in the rat liver, kidney, jejunum, ileum, placenta, and lung. This is the first study on the translational regulatory mechanisms of the MRP2/Mrp2 gene.

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Murphy, Patrick. "Characterisation of critical interactions between translation factors eIF2 and eIF2B." Thesis, University of Manchester, 2013. https://www.research.manchester.ac.uk/portal/en/theses/characterisation-of-critical-interactions-between-translation-factors-eif2-and-eif2b(9138d7c8-34b1-4489-8048-a2ac45ef8533).html.

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Eukaryotic translation initiation is a complex and highly regulated process involving the ribosome, mRNA and proteins called eukaryotic initiation factors (eIFs). The overall aim of translation initiation is to position the ribosome at the initiation codon of the mRNA. eIF2, in its GTP-bound conformation, binds the initiator tRNA (Met-tRNAiMet) and delivers it to the 40S ribosomal subunit. When the anticodon of the tRNA is bound to the initiation codon, the GTP on eIF2 is hydrolysed to GDP. The guanine nucleotide exchange factor (GEF) eIF2B regenerates eIF2-GTP. eIF2 and eIF2B are multisubunit/multidomain protein complexes. Because information regarding the interface between each complex is limited, particularly the interface on the eIF2γ subunit, which binds the guanine-nucleotides and Met-tRNAiMet, interactions between the minimal GEF domain of eIF2Bε, εGEF, and eIF2 were mapped using mutagenesis and an in vitro cysteine cross-linking approach, with the cross-linker Mts-Atf-Biotin. Site-directed mutagenesis (SDM) was used to mutate five N-terminal and five C-terminal surface-exposed εGEF residues to cysteines. The mutant alleles were analysed in Saccharomyces cerevisiae and it was found that the gcd6-R574C allele was lethal and the gcd6-T572C was Gcd-. Further gcd6-R574 mutant alleles were also found to be lethal in yeast but expressed in vivo.εGEF-R574C has dramatically reduced GEF activity in vitro and binding assays showed that this mutant has significantly reduced affinity for eIF2. The εGEF-T572C and εGEF-S576C mutants also have severe and minor eIF2-binding defects respectively, while the C-terminal εGEF-Cys mutants have slightly reduced affinity for eIF2. The N-terminal εGEF-Cys mutants cross-link specifically to eIF2γ, while the C-terminal εGEF-Cys mutants interact predominantly with eIF2β. From the data obtained in this study, we propose a new model for eIF2B-mediated guanine-nucleotide exchange that reduces the importance of eIF2β and suggests εGEF resembles other GEFs in binding primarily to its G protein partner eIF2γ.

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Book chapters on the topic "Translation initiation sites"

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Tzanis, George, and Ioannis Vlahavas. "Prediction of Translation Initiation Sites Using Classifier Selection." In Advances in Artificial Intelligence, 367–77. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/11752912_37.

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Li, Guoliang, Tze-Yun Leong, and Louxin Zhang. "Translation Initiation Sites Prediction with Mixture Gaussian Models." In Lecture Notes in Computer Science, 338–49. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-30219-3_29.

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Gao, Xiangwei, Ji Wan, and Shu-Bing Qian. "Genome-Wide Profiling of Alternative Translation Initiation Sites." In Methods in Molecular Biology, 303–16. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3067-8_19.

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Zeng, Jia, and Reda Alhajj. "Integrating Swarm Intelligent Algorithms for Translation Initiation Sites Prediction." In Innovations in Swarm Intelligence, 141–57. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-04225-6_8.

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Tzanis, George, Christos Berberidis, and Ioannis Vlahavas. "A Novel Data Mining Approach for the Accurate Prediction of Translation Initiation Sites." In Biological and Medical Data Analysis, 92–103. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/11946465_9.

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Vishnevsky, O. V., I. V. Avdeeva, and A. V. Kochetov. "Study of the Specific Contextual Features of Translation Initiation and Termination Sites in Saccharomyces Cerevisiae." In Bioinformatics of Genome Regulation and Structure, 213–22. Boston, MA: Springer US, 2004. http://dx.doi.org/10.1007/978-1-4419-7152-4_23.

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Tzanis, George, Christos Berberidis, Anastasia Alexandridou, and Ioannis Vlahavas. "Improving the Accuracy of Classifiers for the Prediction of Translation Initiation Sites in Genomic Sequences." In Advances in Informatics, 426–36. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/11573036_40.

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de Haro-García, Aida, Javier Pérez-Rodríguez, and Nicolás García-Pedrajas. "Feature Selection for Translation Initiation Site Recognition." In Lecture Notes in Computer Science, 357–66. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-21827-9_37.

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García-Pedrajas, Nicolás, Domingo Ortiz-Boyer, María D. García-Pedrajas, and Colin Fyfe. "Class Imbalance Methods for Translation Initiation Site Recognition." In Trends in Applied Intelligent Systems, 327–36. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-13022-9_33.

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del Castillo-Gomariz, Rafael, and Nicolás García-Pedrajas. "Translation Initiation Site Recognition by Means of Evolutionary Response Surfaces." In Lecture Notes in Computer Science, 376–85. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-21827-9_39.

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Conference papers on the topic "Translation initiation sites"

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Karri, Kritika, and Dhundy R. Bastola. "A novel signature for identification of upstream alternative translation initiation sites." In 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2015. http://dx.doi.org/10.1109/bibm.2015.7359850.

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Sendoel, Ataman, Joshua G. Dunn, Edwin H. Rodriguez, Shruti Naik, Nicholas C. Gomez, Brian Hurwitz, John Levorse, et al. "Abstract 4766: Translation from unconventional 5' start sites drives tumor initiation." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-4766.

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Zeng, Jia, and Reda Alhajj. "Predicting translation initiation sites using a multi-agent architecture empowered with reinforcement learning." In 2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2008). IEEE, 2008. http://dx.doi.org/10.1109/cibcb.2008.4675786.

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Gao, Shi-Bo, and Yun-Tao Zhang. "Optimization of AdaBoost Algorithm by PSO and Its Application in Translation Initiation Sites Prediction." In 2009 WRI Global Congress on Intelligent Systems. IEEE, 2009. http://dx.doi.org/10.1109/gcis.2009.169.

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Huang, Juncai, Fengbi Wang, Yangji Ou, and Mingtian Zhou. "A Semi-supervised SVM Based Incorporation Prior Biological Knowledge for Recognizing Translation Initiation Sites." In 2009 WRI World Congress on Computer Science and Information Engineering. IEEE, 2009. http://dx.doi.org/10.1109/csie.2009.447.

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Li, Haifeng, and Tao Jiang. "A class of edit kernels for SVMs to predict translation initiation sites in eukaryotic mRNAs." In the eighth annual international conference. New York, New York, USA: ACM Press, 2004. http://dx.doi.org/10.1145/974614.974649.

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Ma, Chuang, Dao Zhou, and Yanhong Zhou. "Feature Mining and Integration for Improving the Prediction Accuracy of Translation Initiation Sites in Eukaryotic mRNAs." In 2006 Fifth International Conference on Grid and Cooperative Computing Workshops. IEEE, 2006. http://dx.doi.org/10.1109/gccw.2006.40.

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Wha Lin, Shu, J. Ware, H. Roberts, N. McGraw, W. McAllister, and D. Stafford. "EXPRESSION OF HUMAN FACTOR IX IN MAMMALIAN CELLS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643567.

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Abstract:

Human factor IX has been expressed in mammalian cells. A cloned factor IX cDNA missing the first 15 nucleotides of the 5’ end was modified by in vitro mutagenesis to restore the missing codons and add the translation consensus sequence, CCACC, proposed by Kozak to be optimal for translational initiation. Additionally, Bgl II and BamHI sites were added immediately upstream of the CCACC sequence for ease of portability of the fragment. This modified cDNA was inserted into a bovine papillomavirus (BPV) vector under the control of a mouse met alio thionein promoter. The constructed plasmid pBPV-IX was used to transfect a mouse fibroblast cell line C127. After 3 weeks, the transformed foci were isolated and the established cell lines were grown in the presence or absence of vitamin K. Media was collected at 3 day intervals and assayed for factor IX activity in a one stage clotting assay. A standard curve was constructed using purified human factor IX. Cells grown in the presence of vitamin K (3 mg/L) exhibited an activity equivalent to 350 ng/ml of factor IX in the cell media; no (less than 3 ng/ml) activity was detectable in the absence of vitamin K. A monoclonal antibody column specific for the Ca++ dependent form of human factor IX allowed the isolation of approximately 7 ug of purified factor IX from approximately 100 ml of culture medium. Western blot analysis of the purified factor IX revealed 2 protein bands which reacted with a goat anti-human factor IX antibody as well as a human specific monoclonal antibody. One of the immunoreactive bands migrates with authentic human factor IX and the other migrates slower. This expression system provides a convenient way to produce suitable amounts of factor IX and mutated factor IX protein for functional analyses.

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Zeng, Jia, and Reda Alhajj. "Multi-agent System for Translation Initiation Site Prediction." In 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007). IEEE, 2007. http://dx.doi.org/10.1109/bibm.2007.20.

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Zuallaert, Jasper, Mijung Kim, Yvan Saeys, and Wesley De Neve. "Interpretable convolutional neural networks for effective translation initiation site prediction." In 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2017. http://dx.doi.org/10.1109/bibm.2017.8217833.

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