Relevant bibliographies by topics / Translation biology

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Translation biology'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "Translation biology"

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Keiler, Kenneth C. "Biology oftrans-Translation." Annual Review of Microbiology 62, no. 1 (October 2008): 133–51. http://dx.doi.org/10.1146/annurev.micro.62.081307.162948.

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Windgassen, Merle, Dorothée Sturm, Iván J. Cajigas, Carlos I. González, Matthias Seedorf, Holger Bastians, and Heike Krebber. "Yeast Shuttling SR Proteins Npl3p, Gbp2p, and Hrb1p Are Part of the Translating mRNPs, and Npl3p Can Function as a Translational Repressor." Molecular and Cellular Biology 24, no. 23 (December 1, 2004): 10479–91. http://dx.doi.org/10.1128/mcb.24.23.10479-10491.2004.

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ABSTRACT A major challenge in current molecular biology is to understand how sequential steps in gene expression are coupled. Recently, much attention has been focused on the linkage of transcription, processing, and mRNA export. Here we describe the cytoplasmic rearrangement for shuttling mRNA binding proteins in Saccharomyces cerevisiae during translation. While the bulk of Hrp1p, Nab2p, or Mex67p is not associated with polysome containing mRNAs, significant amounts of the serine/arginine (SR)-type shuttling mRNA binding proteins Npl3p, Gbp2p, and Hrb1p remain associated with the mRNA-protein complex during translation. Interestingly, a prolonged association of Npl3p with polysome containing mRNAs results in translational defects, indicating that Npl3p can function as a negative translational regulator. Consistent with this idea, a mutation in NPL3 that slows down translation suppresses growth defects caused by the presence of translation inhibitors or a mutation in eIF5A. Moreover, using sucrose density gradient analysis, we provide evidence that the import receptor Mtr10p, but not the SR protein kinase Sky1p, is involved in the timely regulated release of Npl3p from polysome-associated mRNAs. Together, these data shed light onto the transformation of an exporting to a translating mRNP.
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Deans, Robert. "Engineering Biology—Accelerating Translation." Genetic Engineering & Biotechnology News 41, no. 1 (January 1, 2021): 44–45. http://dx.doi.org/10.1089/gen.41.01.10.

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Aryanpur, Peyman P., David M. Renner, Emily Rodela, Telsa M. Mittelmeier, Aaron Byrd, and Timothy A. Bolger. "The DEAD-box RNA helicase Ded1 has a role in the translational response to TORC1 inhibition." Molecular Biology of the Cell 30, no. 17 (August 2019): 2171–84. http://dx.doi.org/10.1091/mbc.e18-11-0702.

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Ded1 is a DEAD-box RNA helicase with essential roles in translation initiation. It binds to the eukaryotic initiation factor 4F (eIF4F) complex and promotes 48S preinitiation complex assembly and start-site scanning of 5′ untranslated regions of mRNAs. Most prior studies of Ded1 cellular function were conducted in steady-state conditions during nutrient-rich growth. In this work, however, we examine its role in the translational response during target of rapamycin (TOR)C1 inhibition and identify a novel function of Ded1 as a translation repressor. We show that C-terminal mutants of DED1 are defective in down-regulating translation following TORC1 inhibition using rapamycin. Furthermore, following TORC1 inhibition, eIF4G1 normally dissociates from translation complexes and is degraded, and this process is attenuated in mutant cells. Mapping of the functional requirements for Ded1 in this translational response indicates that Ded1 enzymatic activity and interaction with eIF4G1 are required, while homo-oligomerization may be dispensable. Our results are consistent with a model wherein Ded1 stalls translation and specifically removes eIF4G1 from translation preinitiation complexes, thus removing eIF4G1 from the translating mRNA pool and leading to the codegradation of both proteins. Shared features among DED1 orthologues suggest that this role is conserved and may be implicated in pathologies such as oncogenesis.
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Gough, N. R. "Translation Required for Translational Repression." Science Signaling 2, no. 80 (July 21, 2009): ec249-ec249. http://dx.doi.org/10.1126/scisignal.280ec249.

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Bania*, Allif Syahputra, Nuraini Nuraini, Nursamsu Nursamsu, and Muhammad Yakob. "The Quality of Taxonomy Translation in English Indonesian Latin by Biological Education Students." Jurnal Pendidikan Sains Indonesia 9, no. 4 (October 15, 2021): 694–710. http://dx.doi.org/10.24815/jpsi.v9i4.21562.

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Translation of literacy in english, Indonesian and latin has a strategic position in the biological sciences that must be studied with good quality for students so that the development of science. The purpose of this study is to examine the quality of taxonomy translation in English, Indonesian and Latin with regard to biology education. This research is a quantitative-descriptive research. The test method is used to collect data on the ability to translate in biology education learning by using the google form media provided through the biology student WhatsApp group due to the Covid-19 pandemic in the form of 10 questions with a blend of English, Latin and Indonesian about taxonomy. There are 13 respondents who are ready to answer the test. The test is given for 1 credit which is about 45 minutes as the deadline. The data analysis technique in this study is descriptive quantitative which uses three lines of research activities, namely data reduction, data display, and conclusion drawing/verification.The results obtained by respondents find it easier to translate test questions in short sentences. The quality of taxonomy translations related to English, Indonesian and Latin have good quality because from the first session, namely translation into the target language English, 4 of the total questions were obtained with the percentage of success by students in translating well above 50%. Likewise for the results of the translation with the target language Indonesian, the respondents managed to answer all questions well with a percentage above 50%. Here it can be seen that, translating into the target language Indonesian is still easier for respondents to produce because all questions are of high value than translating into the target language English.
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Zhang, Cuiling. "Neuroscience and Translation." International Journal of Translation and Interpreting Research 15, no. 2 (July 31, 2023): 180–83. http://dx.doi.org/10.12807/ti.115202.2023.r02.

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In the past decades, researchers have established various theories and approaches to explore the nature of translation, this “most complex type of event yet produced in the evolution of the cosmos” (Richard, 1953:250). Especially since the inception of Translation Studies as an academic discipline in the 1970s, translation scholars have drawn extensively on tools, concepts, and theories from other disciplines, such as sociology, anthropology, psychology, and biology in their efforts to explore the many facets of translation and interpreting. Now, neuroscience came to the fore. As the study of the nervous system, the task of neuroscience is to understand brain processes— how we perceive, act, learn, and remember – and explain behavior in terms of brain activities (Kandel et al., 2012, pp. 3-5). For decades, neuroscientists have explored human language and have produced remarkable studies on language development and learning. Yet the findings on how the brain handles language processing are still primarily based on monolinguals. The mental process of multilingual people and many other aspects of the transfer between different languages remain largely unsettled. This inspired Maria Tymoczko to explore the neurological mechanisms involved in translating, a field that she dubs as one of the “known unknowns” in translation studies (Tymoczko, 2012) and believes will fundamentally influence the way translation is thought about and ultimately illuminate many aspects of translation, including the “black box” of the individual translator.
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Weiner, George. "Cancer biology: Lost in translation?" Cancer Biology & Therapy 3, no. 7 (July 2004): 688–91. http://dx.doi.org/10.4161/cbt.3.7.959.

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Gold, Larry. "Translation, genetics and cell biology." Trends in Genetics 3 (January 1987): 236–37. http://dx.doi.org/10.1016/0168-9525(87)90251-4.

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Kiberstis, P. A. "MOLECULAR BIOLOGY: Translation by Entrapment." Science 299, no. 5606 (January 24, 2003): 475a—475. http://dx.doi.org/10.1126/science.299.5606.475a.

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Dissertations / Theses on the topic "Translation biology"

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Chew, Guo-Liang. "Non-Canonical Translation in Vertebrates." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:17467487.

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Translation is a key process during gene expression: to produce proteins, ribosomes translate the coding sequences of mRNAs. However, vertebrate genomes contain more translation potential than these annotated coding sequences: translation has been detected in many non-coding RNAs and in the non-coding regions of mRNAs. To understand the role of such translation in vertebrates, I investigated: 1) the distribution of translation in vertebrate long non-coding RNAs, and 2) the effects of translation in the 5’ leaders of vertebrate mRNAs. To quantify and localize translation in a genome-wide manner, we produced and analyzed ribosome profiling data in zebrafish, and analyzed ribosome profiling data produced by others. The nucleotide resolution afforded by ribosome profiling allows localization of translation to individual ORFs within a transcript, while its quantitative nature enables measurement of how much translation occurs within individual ORFs. We combined ribosome profiling with a machine-learning approach to classify lncRNAs during zebrafish development and in mouse ES cells. We found that dozens of proposed lncRNAs are protein-coding contaminants and that many lncRNAs have ribosome profiles that resemble that of the 5’ leaders of coding mRNAs. These results clarify the annotation of lncRNAs and suggest a potential role for translation in lncRNA regulation. Because much of the translation in non-coding regions of mRNAs occurs within uORFs, we further examined the effects of their translation on the cognate gene expression. While much is known about the repression of individual genes by their uORFs, how uORF repressiveness varies within a genome and what underlies this variation had not been characterized. To address these questions, we analyzed transcript sequences and ribosome profiling data from human, mouse and zebrafish. Linear modeling revealed that sequence features at both uORFs and coding sequences contribute similarly and substantially toward modulating uORF repressiveness and coding sequence translational efficiency. Strikingly, uORF sequence features are conserved in mammals, and mediate the conservation of uORF repressiveness in vertebrates. uORFs are depleted near coding sequences and have initiation contexts that diminish their translation. These observations suggest that the prevalence of vertebrate uORFs may be explained by their functional conservation as weak repressors of coding sequence translation.
Biology, Molecular and Cellular
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Lin, Chen-ju. "Targeting translation initiation for cancer therapy." Thesis, McGill University, 2011. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=96981.

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The recruitment of ribosomes to the 5' end of mRNAs in eukaryotic cells is generally thought to be the rate-limiting step of translation initiation and this process is mediated by the eukaryotic initiation factor 4F complex (eIF4F). This complex consists of three subunits: eIF4E, a mRNA-cap binding protein, eIF4A, a RNA helicase and eIF4G, a large molecular scaffold that mediates the binding of mRNA to ribosomes. Deregulation of translation initiation through eIF4F activation has been widely observed in human cancers. The eIF4F complex lies downstream of key signalling pathways involved in oncogenesis (such as c-Myc and PI3K/Akt/mTOR), thus targeting translation initiation provides an attractive therapeutic approach for cancer therapy. Here, we show that c-Myc stimulates protein synthesis by up-regulating the expression and activity of not only eIF4E, but that of the other two subunits of eIF4F. In turn, this elevated eIF4F levels result in increased synthesis and function of c-Myc, establishing a positive feedforward loop. We used the Eμ-myc lymphoma mouse model to show that expression of the three eIF4F subunits is also up-regulated by c-Myc in vivo. Most importantly, we demonstrate that loss of eIF4E function using inducible and reversible RNA interference (RNAi) greatly delays the rates of c-Myc-induced lymphoma development. These data suggest that targeting eIF4E in vivo is an effective therapeutic approach. Since the assembly of eIF4F complex is regulated by mTOR signaling, the coupling of c-Myc to eIF4F is under mTOR control. In the course of a screen of inhibitors of the PI3K/Akt/mTOR signalling pathway, we found two small molecules, silibinin and the anti-depressant sertraline, both of which show anti-proliferative effects on breast cancer cells. Silibinin and sertraline effectively target eIF4F complex function by downregulating mTOR signaling. Importantly, sertraline is able to enhance the chemosensitivity of PTEN (+/-)/Eμ-Myc lymphomas to the chemotherapeutic agent doxorubicin in vivo. Thus, targeting mTOR-dependent translation initiation shows anti-cancer activity in this pre-clinical setting.
Il est généralement admis que le recrutement des ribosomes à l'extrémité 5' des ARN messagers (ARNm) est l'étape limitante de l'initiation de la traduction chez les eucaryotes. Cette étape est dépendante de l'activité du complexe d'initiation eIF4F qui comprend trois sous-unités: eIF4E, une protéine liant la coiffe des ARNm, eIF4A, une hélicase d'ARN et eIF4G, une grande protéine d'échafaudage dont le rôle est de coordonner la liaison du ribosome à l'ARNm. Le dérèglement du contrôle de l'initiation de la traduction suite à l'activation d'eIF4F est observé fréquemment chez les cancers humains. L'activité de ce complexe est contrôlée par plusieurs voies de signalisation clés qui sont impliquées dans la formation des tumeurs (tels que c-Myc et PI3K/Akt/mTOR). Donc, cibler l'initiation de la traduction représente une avenue attrayante pour contrer le cancer. Nous démontrons ici que l'oncogène c-Myc peut stimuler la synthèse protéique en favorisant l'expression et l'activité de non-seulement eIF4E, mais aussi des deux autres sous-unités du complexe eIF4F. En réponse à cela, les niveaux supérieurs d'eIF4F permettent une augmentation de la synthèse et donc de l'activité de c-MYC, établissant alors une boucle auto-stimulante. Nous avons utilisé le modèle de souris Eμ-myc pour démontrer que l'expression de chacune des sous-unités d'eIF4F est stimulée par c-Myc in vivo. Plus important encore, nous avons démontré que la réduction des niveaux d'eIF4E en utilisant la technique d'interférence à ARN (ARNi) de manière inductible et réversible freine considérablement le développement de lymphomes par c-Myc. Ces données suggèrent que cibler eIF4E in vivo est une approche thérapeutique viable et efficace. De plus, puisque l'assemblage d'eIF4E est contrôlé de mTOR, il en résulte donc que le couplage de c-Myc et d'eIF4F est donc aussi sous contrôle de cette voie de signalisation. Suite à un cribblage de molécules inhibitrices de la voie PI3K/Akt/mTOR, nous avons identifié deux molécules, la silibinine et l'anti-dépresseur sertraline, qui ont la propriété de bloquer la prolifération de cellules du cancer du sein. La silibinin et la sertraline inhibent efficacement l'activité du complexe eIF4F en ciblant la voie de signalisation de mTOR. Par surcroît, la sertraline accentue fortement la sensibilité des lymphomes PTEN (+/-)/Eμ-Myc à l'agent chimiothérapeutique doxorubicin in vivo. En conclusion, il appert que cibler le contrôle de la traduction par mTOR peut contrer efficacement le cancer dans ce modèle de cancer préclinique.
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Kinney, Emma. "Decoupling of HSV1 Vhs protein mRNA decay and translation stimulation." Thesis, University of Missouri - Kansas City, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=1543940.

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Herpes Simplex Virus Type 1 is a member of the alphaherpesvirinae subfamily within the family Herpesviridae. This virus has both a lytic and latent cycle. Primary infection occurs when the virus enters epithelial cells around the mucosal lining of the nose and mouth. Within the epithelial cells, the virus undergoes an active lytic infection, causing an ulcerated blister, more famously known as a 'cold sore' or 'fever blister'. Once HSV enters the nearby sensory neurons the genome is transported to the neuronal cell body where its latency associated transcripts are activated and the virus remains in a dormant latent cycle until reactivation, when the virus is transported back down the axon to the epithelial cells at or near the site of initial infection. The Virion Host Shutoff protein is a tegument protein from HSV1 and acts as a ribonuclease, degrading both cellular and viral mRNAs, making the course of viral infection more efficient. A study by Saffran, Read and Smiley uncovered an unexpected new function of Vhs: stimulation of translation from some IRESs. An IRES is a section of mRNA with a high level of secondary structure, capable of inducing cap-independent translation. In similar experiments utilizing a bicistronic reporter transcript, I sought to discover whether or not these two functions of the Vhs protein could be de-coupled. Experiments involved dually transfecting HeLa cells with different Vhs mutants across a range of Vhs plasmid concentrations and the bicistronic reporter construct. Levels of reporter activity were measured from cell lysates 36 hours after transfections and provided a measurement of the control at the level of translation. As the cellular Bip IRES element was present between the cistrons, the 3' cistron provided a measure of IRES stimulation. The Results revealed examples of Vhs mutants in which the two activities had been separated. It is unknown what role IRES stimulation could play during Herpesvirus infection, although it is interesting to note that some HSV1 genes have IRES like elements within the 5' UTR. Future experiments can be done to investigate whether or not Vhs is actively recruiting transcription initiation factors to these IRES elements.

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Cho, Park 1975. "The Cap-binding inhibitor of translation, d4EHP /." Thesis, McGill University, 2005. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=111819.

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In eukaryotes, the initiation phase of protein synthesis or translation is a multi-step process that culminates in the positioning of the SOS ribosome at the initiation codon of a messenger RNA (mRNA). Recognition of the cap structure by eukaryotic initiation factor 4F (etF4F; composed of three subunits: the cap-binding protein e1F4E, the RNA-helicase eIF4A and the scaffolding protein eIF4G) facilitates this process. The ability of eIF4F to bind to the cap, as a result of the Cap:eIF4E interaction is of particular importance, as it is the major target of translational regulatory mechanism.
Early embryogenesis requires the activity of various maternal determinants called morphogens, whose spatial and temporal expressions are tightly regulated at the level of translation. Positional information encoded within these factors is thus important for the establishment of body polarity. For instance, in Drosophila, when maternal Caudal (Cad) and Hunchback (Hb) proteins are allowed to accumulate inappropriately in an embryo, anterior and abdominal segmentations are blocked. Hence, the precision of Cad and Hb expression domains is critical for normal development.
An eIF4E-related protein called eIF4E-Homologous protein (4EHP) was first described in 1998. However, the function, if any, of 4EHP in translation has been elusive, since it does not interact with any known initiation factors. In order to elucidate its biological function, the power of Drosophila genetics was used. In this thesis, I show that the Drosophila homolog of 4EHP (d4EHP) interacts with Bicoid (Bcd) and Brain tumor (Brat) proteins to inhibit the translation of maternal cad and hb mRNAs. Simultaneous interaction of d4EHP with the cap and Bcd or Brat results in mRNA circularization, which renders cad and hb mRNAs translationally inactive. This example of cap-dependent translational control that is not mediated by eIF4E defines a new paradigm for translational inhibition involving tethering of the mRNA 5' and 3' ends.
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Malina, Abba. "The therapeutic potential in eukaryotic mRNA translation." Thesis, McGill University, 2013. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=114176.

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Inhibitors of translation have proven invaluable in delineating the overall mechanism of protein synthesis. Unlike inhibitors of prokaryotic protein synthesis, the therapeutic development of drugs that directly interfere in the eukaryotic mRNA translation for treatment of human disease has remained largely unexplored. To begin to investigate this possibility and expand the current repertoire of compounds that affect eukaryotic translation, we have undertaken several different experimental screening approaches, two of which are described below and will form the basis of this thesis. In chapter 2, we performed a multiplexed high-throughput chemical screen to identify novel inhibitors of eukaryotic protein synthesis. We identified intercalators as having unique biological properties in our assays: at high concentrations they behave like elongation inhibitors and blocked the peptidyl-transferase activity of the ribosome, while at lower concentrations they preferentially block HCV-driven, cap-independent but not cap-dependent translation. This activity appeared to be due to their ability to block the innate affinity of the HCV IRES for the 40S ribosomal subunit. Moreover, a number of intercalator-based peptide-conjugates (which can chemically "thread" through and bind strands of nucleic acid in a sequence-specific manner) were tested and one, PAC-6, was found to be a selective inhibitor of HCV-dependent initiation.In chapter 3, we performed a shRNA-based drop-out screen to identify novel genes and pathways that could reverse resistance to ABT-737 treatment. Using genetically-defined Arf-/-Eµ-myc lymphoma cells, pools of shRNAs targeting known factors and regulators of protein synthesis were retrovirally introduced and genomic DNA collected over the course 10 days for both vehicle and ABT-737 treated cohorts. Following deep sequencing analysis of shRNA abundance, several constructs were identified that were selectively depleted only in the presence of ABT-737. Of them, two shRNAs against the RNA/DNA helicase, DHX9, validated. Although knockdown of DHX9 was found to sensitize both mouse and human cells to ABT-737 treatment, it did so without altering Mcl-1 levels. Instead, loss of DHX9 appeared to activate a p53-dependent apoptotic program which was found to be both necessary and sufficient for the ABT-737-shDHX9 synthetic lethal interaction.
La compréhension du mécanisme global de la synthèse protéique a rapidement progressée en majeur partie grâce a l'utilisation d'inhibiteurs spécifiques qui bloquent ce processus. Contrairement aux inhibiteurs de la synthèse protéique procaryote, l'utilisation de molécules pouvant moduler la traduction des ARNm eucaryotes dans un but thérapeutique reste encore largement sous-évalué. Afin d'étudier cette possibilité et d'élargir le répertoire de composés chimiques pouvant interférer avec la synthèse protéique eucaryote, nous avons effectué plusieurs criblage différents. Deux d'entre eux sont décrits plus bas et formeront les fondements de cette thèse.Tel que décrit dans le chapitre 2, nous avons tout d'abord effectué un criblage à haut débit de molécules afin d'identifier de nouveaux inhibiteurs de la synthèse protéique eucaryote. Ceci nous a permis de découvrir que les molécules qui peuvent s'intercaler dans les structures en double brin des acides nucléiques possèdent des propriétés uniques d'inhibition de la traduction. En effet, à hautes concentrations, elles se comportent exactement comme des inhibiteurs de l'élongation et bloquent l'activité peptidyl-transférase des ribosomes, alors qu'à faibles concentrations, elles bloquent préférentiellement la traduction cap-indépendant sous contrôle de l'IRES de HCV sans affecter la traduction dépendante du cap. Cette activité semble être due à la capacité des molécules d'interférer avec la liaison de la sous-unité 40S à l'IRES de HCV. De plus, certaines molécules qui combinent une portion intercalatrice et une portion peptidique (connue pour pouvoir sonder et se lier spécifiquement des brins d'acides nucléiques de manière spécifique) ont été testées et une d'entre elles, nommé PAC-6, permet l'inhibition spécifique de l'initiation de la traduction sous contrôle de l'IRES de HCV.Dans le chapitre 3, nous avons effectué un criblage d'une librairie de shRNA afin d'identifier des gènes ou des voies de signalisation qui peuvent inverser la résistance de cellules à ABT-737. Des cellules de lymphomes Arf-/-Eµ-Myc génétiquement modifiées ont été infecté avec un groupe de shRNAs ciblant des gènes connus pour contrôler tous les aspects de la synthèse protéique et avons isolé l'ADN génomique de ces cellules après 10 jours de traitements avec, soit le véhicule, soit avec ABT-737. Suite à l'analyse de l'abondance relative des shRNAs par séquençage de nouvelle génération, nous en avons identifié plusieurs dont la représentation diminue sélectivement en présence d'ABT-737. Parmi ceux-ci, deux shRNAs uniques, ciblant l'hélicase à ARN/ADN DHX9 ont été identifiés et par la suite confirmés indépendamment. La diminution des niveaux de DHX9 permet la sensibilisation des cellules murines ou humaines à ABT-737 sans toutefois altérer les niveaux de Mcl-1. Plutôt, la perte de DHX9 semble activer un programme d'apoptose dépendant de p53 qui est nécessaire et suffisant pour cette interaction synthétique létale entre ABT-737 et DHX9.
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Chiappetta, Margaret Elizabeth. "Knowledge translation in action : cancer biology and systems pharmacology at the National Center for Advancing Translational Science." Thesis, University of British Columbia, 2014. http://hdl.handle.net/2429/50189.

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The need for novel diagnostic and therapeutic drugs with the potential to combat increasingly prevalent or particularly insidious diseases has grown in recent years. Concurrently, the issue of translating scientific knowledge from “bench to bedside” has become increasingly salient. In 2011, the U.S. National Institutes of Health created the National Center for Advancing Translational Science in an effort to remedy the recalcitrant gaps between fundamental laboratory research and late-stage clinical trial, thereby dramatically reducing the amount of time and expense needed to develop efficacious pharmaceutical prototypes for a range of emerging, re-emerging, and chronic diseases. However, the realities of pharmaceutical development are incongruous with the expectations of the lay public that even the most fundamental scientific research yield results with immediate social and commercial value. Traditional linear models of progress overlook both the epistemic nature of scientific innovation and the significance of the socio-economic supply and demand factors driving research endeavours. The aim of this dissertation is to underline the epistemic and socio-economic characteristics of translational science – specifically in the context of research targeting novel oncology therapeutics and diagnostics – through the lens of Science and Technology Studies. In focusing on research in cancer biology funded by the National Center for Advancing Translational Science, this thesis highlights the significance of Mode 2 or “post-academic” science, and by extension the roles of interdisciplinarity and applicability, and the commodification of scientific knowledge, that arise in the process of translating scientific knowledge.
Arts, Faculty of
Graduate
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Yao, Xiaoquan. "Sequence features affecting translation initiation in eukaryotes: A bioinformatic approach." Thesis, University of Ottawa (Canada), 2008. http://hdl.handle.net/10393/27658.

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Sequence features play an important role in the regulation of translation initiation. This thesis focuses on the sequence features affecting eukaryotic initiation. The characteristics of 5' untranslated region in Saccharomyces cerevisiae were explored. It is found that the 40 nucleotides upstream of the start codon is the critical region for translation initiation in yeast. Moreover, this thesis attempted to solve some controversies related to the start codon context. Two key nucleotides in the start codon context are the third nucleotide upstream of the start codon (-3 site) and the nucleotide immediately following the start codon (+4 site). Two hypotheses regarding +4G (G at +4 site) in Kozak consensus, the translation initiation hypothesis and the amino acid constraint hypothesis, were tested. The relationship between the -3 and +4 sites in seven eukaryotic species does not support the translation initiation hypothesis. The amino acid usage at the position after the initiator (P1' position) compared to other positions in the coding sequences of seven eukaryotic species was examined. The result is consistent with the amino acid constraint hypothesis. In addition, this thesis explored the relationship between +4 nucleotide and translation efficiency in yeast. The result shows that +4 nucleotide is not important for translation efficiency, which does not support the translation initiation hypothesis. This work improves our current understanding of eukaryotic translation initiation process.
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Fung, Hiu Leong. "Human C7orf30 is a novel mitochondrial translation factor." Thesis, McGill University, 2011. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=103744.

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Mitochondria generate the majority of cellular energy through oxidative phosphorlyation. The machinery of oxidative phosphroylation consists of five enzyme complexes that are located in the inner mitochondrial membrane. A small number of essential subunits in these complexes are encoded by mtDNA and synthesized on a dedicated mitochondrial translation apparatus. Defects in mitochondrial translation system cause many mitochondrial diseases, but the mechanisms that regulate mitochondrial translation remain largely unknown. We have identified an unnamed human protein C7orf30, as a possible mitochondrial translation factor. The orthologue of C7orf30 in maize is thought to be a chloroplast ribosome assembly factor. We identified human C7orf30 to be a mitochondrial protein through bioinformatics analysis and immunocytochemistry. We knocked down the expression of C7orf30 in human fibroblast using shRNA and observed a reduction in cytochrome c oxidase activity. Using a translation assay, we observed a global reduction in the synthesis of mitochondrially encoded proteins when C7orf30 was knocked down, while the transcript levels were not affected. The assembly of Complex I, III, IV and V also demonstrated defects. Sucrose density gradient analysis suggests C7orf30 interacts with 39S subunit of the mitoribosome. The assembly of the mitoribosome and the levels of 12S and 16S MT-rRNA were not affected by C7orf30 knockdown, suggesting C7orf30 is not necessary for mitochondrial ribosome assembly. We hypothesize that C7orf30 interacts with the mitoribosome and is a regulator of mitochondrial translation.
Les mitochondries génèrent la majorité de l'énergie cellulaire grâce à l'oxydation phosphorylative. La chaîne respiratoire responsable de ce phénomène est composée de cinq complexes enzymatiques localisés dans la membrane interne de la mitochondrie. Certaines des sous-unités essentielles de ces complexes sont codées par l'ADN mitochondrial. Leur synthèse est assurée par la mitochondrie qui possède son propre système de traduction des protéines. Les déficiences de la traduction mitochondriale sont à l'origine de nombreuses maladies et les mécanismes qui régulent le processus de traduction restent à ce jour peu élucidés. Dans cette étude, nous avons identifié chez l'homme, C7orf30, une protéine probablement impliquée dans la régulation de la traduction mitochondriale. Il existe un homologue de cette protéine chez le maïs. Une étude suggère son rôle en tant que facteur d'assemblage des ribosomes des chloroplastes. Des programmes informatiques prédisent la localisation de la protéine C7orf30 humaine dans la mitochondrie ce que nous avons confirmé par des expériences d'immunocytochimie. L'utilisation de shRNA dirigés contre C7orf30 dans des fibroblastes humains révéle d'abord une réduction de l'activité cytochrome c oxydase (complexe IV). Des expériences de traduction ex vivo montrent ensuite une réduction globale de la synthèse des protéines codées par la mitochondrie dans les cellules déficitaires en C7orf30, la transcription étant normale. L'assemblage des complexes I, III, IV et V de la chaîne respiratoire est également affecté. La séparation des protéines par gradient de sucrose suggère que C7orf30 interagit avec la sous unité 39S des ribosomes mitochondriaux. Cependant, l'assemblage et les niveaux d'expression des rRNA 12S et 16S ne sont pas affectés par la diminution de la protéine ce qui suggère qu'elle n'est pas indispensable à l'assemblage des ribosomes mitochondriaux en soit. Dans cette étude, nous émettons l'hypothèse que C7orf30 est un composant du ribosome et agit comme un régulateur de la traduction mitochondriale.
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Arribere, Joshua A. (Joshua Alexander). "Transcript leaders : annotation and insight into functions in translation." Thesis, Massachusetts Institute of Technology, 2013. http://hdl.handle.net/1721.1/83763.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2013.
CD-ROM contains PDF of title page and .txt of tables.
Cataloged from PDF version of thesis. Vita.
Includes bibliographical references.
For a eukaryotic mRNA to be properly expressed, it undergoes a series of several steps, including transcription, modification, splicing, packaging, export, localization, translation, and decay. Of these steps transcription is the most extensively studied, though the remaining steps are also indispensible for proper protein production. While we understand many of these steps in biochemical detail in vitro, we have a much poorer knowledge of how they occur and are regulated for a given gene in vivo. Posttranscriptional regulation is carried out primarily through the noncoding portions of the mRNA: the Transcript Leader (TL or 5'UTR) upstream of the Open Reading Frame (ORF), and the 3'Untranslated Region (3'UTR) downstream. To understand how these regions affect post-transcriptional gene expression, it is critical to have precise annotations of the mRNA(s) produced from a gene. In Chapter 2 I describe the development of Transcript Leader Sequencing (TL-seq), a technique to annotate TLs, and demonstrate its utility in yeast. TL-seq annotations reveal interesting TL-dependent regulation, including transcription within ORFs and short TLs that are associated with translation initiation at the second AUG of the ORE. To further study the roles of TLs in translation, I develop Translation-Associated Transcript Leader Sequencing (TATL-seq). TATL-seq works by applying TL-seq across fractions of a polysome gradient, generating TL-specific translational measurements. This approach demonstrates a widespread inhibitory function for upstream AUGs (uAUGs), and that ~6% of yeast genes express multiple TL species with distinct translational activities. This demonstrates that alternative TLs are prevalent and functional even in a relatively simple eukaryote like yeast. My interest in alternative TLs prompted me to explore TL variation in mammals, where many thousands of genes are known to have alternative TLs. In Chapter 3 I enumerate the contributions of alternative mRNA processing events to alternative TLs in mice. I observe alternative TLs produced by alternative Transcription Start Sites (TSSs), and also demonstrate that alternative splicing events, such as skipped exons and alternative splice sites, contribute substantially to functional TL diversity. To facilitate the future study of alternative TLs in mammals, in Appendix I I modify TL-seq to sequence longer TL fragments and optimize TL-seq's enzymatic steps to reduce input RNA requirements. This thesis is concerned with understanding post-transcriptional mRNA expression both globally and gene-specifically. In particular, I seek to understand the role the Transcript Leader has in affecting translation and degradation of its transcript. The findings detailed here define and analyze discernable features of TLs that relate to translational properties of the downstream message. Furthermore, the techniques developed enable analyses of TLs and translation that could not be carried out with previous technologies.
by Joshua A. Arribere.
Ph.D.
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10

Cacan, Ercan. "Evolutionary synthetic biology: structure/function relationships within the protein translation system." Thesis, Georgia Institute of Technology, 2011. http://hdl.handle.net/1853/45838.

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Production of mutant biological molecules for understanding biological principles or as therapeutic agents has gained considerable interest recently. Synthetic genes are today being widely used for production of such molecules due to the substantial decrease in the costs associated with gene synthesis technology. Along one such line, we have engineered tRNA genes in order to dissect the effects of G:U base-pairs on the accuracy of the protein translation machinery. Our results provide greater detail into the thermodynamic interactions between tRNA molecules and an Elongation Factor protein (termed EF-Tu in bacteria and eEF1A in eukaryotes) and how these interactions influence the delivery of aminoacylated tRNAs to the ribosome. We anticipate that our studies not only shed light on the basic mechanisms of molecular machines but may also help us to develop therapeutic or novel proteins that contain unnatural amino acids. Further, the manipulation of the translation machinery holds promise for the development of new methods to understand the origins of life. Along another line, we have used the power of synthetic biology to experimentally validate an evolutionary model. We exploited the functional diversity contained within the EF-Tu/eEF1A gene family to experimentally validate the model of evolution termed ‘heterotachy’. Heterotachy refers to a switch in a site’s mutational rate class. For instance, a site in a protein sequence may be invariant across all bacterial homologs while that same site may be highly variable across eukaryotic homologs. Such patterns imply that the selective constraints acting on this site differs between bacteria and eukaryotes. Despite intense efforts and large interest in understanding these patterns, no studies have experimentally validated these concepts until now. In the present study, we analyzed EF-Tu/eEF1A gene family members between bacteria and eukaryotes to identify heterotachous patterns (also called Type-I functional divergence). We applied statistical tests to identify sites possibly responsible for biomolecular functional divergence between EF-Tu and eEF1A. We then synthesized protein variants in the laboratory to validate our computational predictions. The results demonstrate for the first time that the identification of heterotachous sites can be specifically implicated in functional divergence among homologous proteins. In total, this work supports an evolutionary synthetic biology paradigm that in one direction uses synthetic molecules to better understand the mechanisms and constraints governing biomolecular behavior while in another direction uses principles of molecular sequence evolution to generate novel biomolecules that have utility for industry and/or biomedicine.
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Books on the topic "Translation biology"

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Molecular biology of cancer: Translation to the clinic. Amsterdam [etc.]: Elsevier Academic press, 2010.

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Parsyan, Armen, ed. Translation and Its Regulation in Cancer Biology and Medicine. Dordrecht: Springer Netherlands, 2014. http://dx.doi.org/10.1007/978-94-017-9078-9.

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Zhao, Robert Chunhua, ed. Essentials of Mesenchymal Stem Cell Biology and Its Clinical Translation. Dordrecht: Springer Netherlands, 2013. http://dx.doi.org/10.1007/978-94-007-6716-4.

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Zhao, Robert Chunhua. Essentials of mesenchymal stem cell biology and its clinical translation. Dordrecht: Springer, 2013.

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Jon, Lorsch, ed. Translation initiation: Cell biology, high-throughput methods, and chemical-based approaches. San Diego, Calif: Academic Press, 2007.

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J, Tymms Martin, ed. In vitro transcription and translation protocols. Totowa, N.J: Humana Press, 1995.

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Protein synthesis and translational control: A subject collection from Cold Spring Harbor perspectives in biology. Cold Spring Harbor, N.Y: Cold Spring Harbor Laboratory Press, 2012.

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H.G. Bronn, Ernst Haeckel, and the origins of German Darwinism: A study in translation and transformation. Cambridge, Mass: MIT Press, 2008.

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Sophia, Kapetanaki, and Sharples R. W, eds. Supplementa problematorum: A new edition of the Greek text with introduction and annotated translation. Berlin: Walter de Gruyter, 2006.

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Carus, Titus Lucretius. Lucy Hutchinson's translation of Lucretius, De rerum natura. London: Duckworth, 1996.

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Book chapters on the topic "Translation biology"

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Zlatanova, Jordanka, and Kensal E. van Holde. "Translation." In Molecular Biology, 395–420. 2nd ed. Boca Raton: Garland Science, 2023. http://dx.doi.org/10.1201/9781003132929-15.

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Zlatanova, Jordanka, and Kensal E. van Holde. "Translation." In Molecular Biology, 421–46. 2nd ed. Boca Raton: Garland Science, 2023. http://dx.doi.org/10.1201/9781003132929-16.

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Zlatanova, Jordanka, and Kensal E. van Holde. "Regulation of Translation." In Molecular Biology, 447–76. 2nd ed. Boca Raton: Garland Science, 2023. http://dx.doi.org/10.1201/9781003132929-17.

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Asano, Katsura. "Translation Initiation." In Encyclopedia of Systems Biology, 2263–67. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_820.

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Asano, Katsura, and Koichi Ito. "Translation Elongation." In Encyclopedia of Systems Biology, 2259–63. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_821.

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Saito, Kazuki, and Koichi Ito. "Translation Termination." In Encyclopedia of Systems Biology, 2271–75. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_822.

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Nickelsen, Jörg, Alexandra-Viola Bohne, and Peter Westhoff. "Chloroplast Gene Expression—Translation." In Plastid Biology, 49–78. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1136-3_2.

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Shreve, Gregory M. "Chapter 2. The strange attractions of translation." In American Translators Association Scholarly Monograph Series, 15–38. Amsterdam: John Benjamins Publishing Company, 2023. http://dx.doi.org/10.1075/ata.xx.02shr.

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The complex-adaptive systems model is useful for understanding translational behavior and cognition in a way that unites our discipline with others (economics, biology, psychology) investigating complex, non-linear, dynamical, and adaptive systems. We can recast some conceptions of the development of translation expertise and the methods and strategies of translation pedagogy using the metalanguage and concepts of complexity theory. Donald Kiraly realized this earlier, and this article extrapolates upon his innovative work. In particular, we examine the role of boundary conditions and “strange attractors” in the systemic emergence of behavioral patterns such as Halverson’s “default translations.” We examine how introducing new attractors as “lever points” can disrupt student translational systems and cause them to shift and settle into more pedagogically desirable phase spaces.
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Peled-Zehavi, Hadas, and Avihai Danon. "Translation and translational regulation in chloroplasts." In Cell and Molecular Biology of Plastids, 249–81. Berlin, Heidelberg: Springer Berlin Heidelberg, 2007. http://dx.doi.org/10.1007/4735_2007_0234.

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Romano, M. Carmen, and Ian Stansfield. "Release Factor, Translation." In Encyclopedia of Systems Biology, 1844–45. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_1280.

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Conference papers on the topic "Translation biology"

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Jung, Gyoo Yeol, Sang Woo Seo, Jina Yang, and Byung Eun Min. "Synthetic Biology around Translation Process." In 14th Asia Pacific Confederation of Chemical Engineering Congress. Singapore: Research Publishing Services, 2012. http://dx.doi.org/10.3850/978-981-07-1445-1_072.

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suzuki, kakeru. "Establishment of an in vitro translation system from rice callus extracts." In ASPB PLANT BIOLOGY 2020. USA: ASPB, 2020. http://dx.doi.org/10.46678/pb.20.1052637.

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Khlebodarova, T. M., V. V. Kogai, and V. A. Likhoshvai. "On the Chaotic Potential of the Local Translation at Activated Synapses." In Mathematical Biology and Bioinformatics. Pushchino: IMPB RAS - Branch of KIAM RAS, 2018. http://dx.doi.org/10.17537/icmbb18.6.

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Minaee, Shervin, and Yao Wang. "Fingerprint recognition using translation invariant scattering network." In 2015 IEEE Signal Processing in Medicine and Biology Symposium (SPMB). IEEE, 2015. http://dx.doi.org/10.1109/spmb.2015.7405471.

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Cho, Hsing-Yi. "Ethylene modulates the dynamics of translation via GCN2 and EIN2 in Arabidopsis under submergence." In ASPB PLANT BIOLOGY 2020. USA: ASPB, 2020. http://dx.doi.org/10.46678/pb.20.1332526.

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Kitney, Richard I. "Synthetic Biology – a Key Driver of the BioEconomy through BioDesign and Industrial Translation." In The 4th World Congress on New Technologies. Avestia Publishing, 2018. http://dx.doi.org/10.11159/icbb18.1.

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Hou, Yuemin, and Ji Linhong. "Gene Transcription and Translation in Design." In ASME 2015 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/detc2015-46128.

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An organism grows from very small to the whole body, while an engineering product is assembled from elements. An organism is formed autonomously and adaptable to his/her/its environment, while an engineering product can only execute very limited actions. The formation of a product determines its functionality. Nature is the best teacher for learning how structures are formed for specific functionality. This paper compares the design process with the developmental process of embryo and proposes a qualitative development framework that simulates the gene transcription and translation in biology. The key step in design is transforming behaviors to structures. This is a process from information to the form and it bears some similarity with the process from DNA to the protein in embryogenesis. Three basic steps are required from DNA to the protein: gene transcription, transport and protein synthesis, which is named as gene expression. Key mechanisms contributing to this transformation process are investigated and a qualitative development framework are constructed for a growth design process. Simple examples are presented for illustration of proposed methods.
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Li, Yulin, Jun Seita, Dean Felsher, and David Dill. "Abstract A2-35: Discovery of differentiation therapeutics using a systems biology approach." In Abstracts: AACR Special Conference: Translation of the Cancer Genome; February 7-9, 2015; San Francisco, CA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.transcagen-a2-35.

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Wendel, Hans-Guido. "Abstract IA06: Oncogenic translation programs." In Abstracts: AACR Special Conference on Translational Control of Cancer: A New Frontier in Cancer Biology and Therapy; October 27-30, 2016; San Francisco, CA. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.transcontrol16-ia06.

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Ogier, Stephen E., and Steven M. Wright. "A frequency translation approach for multichannel 13C spectroscopy." In 2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). IEEE, 2015. http://dx.doi.org/10.1109/embc.2015.7318671.

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Reports on the topic "Translation biology"

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Eckdahl, Anthony J., Rachel Neal, A. Malcolm Campbell, and Todd T. Eckdahl. rClone: A Synthetic Biology Tool That Enables the Research of Bacterial Translation. Journal of Young Investigators, March 2017. http://dx.doi.org/10.22186/jyi.32.3.7-12-19.

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Kriegel, Francesco. Learning General Concept Inclusions in Probabilistic Description Logics. Technische Universität Dresden, 2015. http://dx.doi.org/10.25368/2022.220.

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Probabilistic interpretations consist of a set of interpretations with a shared domain and a measure assigning a probability to each interpretation. Such structures can be obtained as results of repeated experiments, e.g., in biology, psychology, medicine, etc. A translation between probabilistic and crisp description logics is introduced and then utilised to reduce the construction of a base of general concept inclusions of a probabilistic interpretation to the crisp case for which a method for the axiomatisation of a base of GCIs is well-known.
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