Relevant bibliographies by topics / Ribosomas

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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 'Ribosomas'

Author: Grafiati
Published: 4 June 2021
Last updated: 6 February 2022

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Journal articles on the topic "Ribosomas"

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Jovanovic, Bogdan, Lisa Schubert, Fabian Poetz, and Georg Stoecklin. "Tagging of RPS9 as a tool for ribosome purification and identification of ribosome-associated proteins." Archives of Biological Sciences, no. 00 (2020): 57. http://dx.doi.org/10.2298/abs20120557j.

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Ribosomes, the catalytic machinery required for protein synthesis, are comprised of 4 ribosomal RNAs and about 80 ribosomal proteins in mammals. Ribosomes further interact with numerous associated factors that regulate their biogenesis and function. As mutations of ribosomal proteins and ribosome associated proteins cause many diseases, it is important to develop tools by which ribosomes can be purified efficiently and with high specificity. Here, we designed a method to purify ribosomes from human cell lines by C-terminally tagging human RPS9, a protein of the small ribosomal subunit. The tag consists of a flag peptide and a streptavidin-binding peptide (SBP) separated by the tobacco etch virus (TEV) protease cleavage site. We demonstrate that RPS9-Flag-TEV-SBP (FTS) is efficiently incorporated into the ribosome without interfering with regular protein synthesis. Using HeLa-GFP-G3BP1 cells stably expressing RPS9-FTS or, as a negative control, mCherry-FTS, we show that complete ribosomes as well as numerous ribosome-associated proteins are efficiently and specifically purified following pull-down of RPS9-FTS using streptavidin beads. This tool will be helpful for the characterization of human ribosome heterogeneity, post-translational modifications of ribosomal proteins, and changes in ribosome-associated factors after exposing human cells to different stimuli and conditions.
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Akanuma, Genki. "Diverse relationships between metal ions and the ribosome." Bioscience, Biotechnology, and Biochemistry 85, no. 7 (April 20, 2021): 1582–93. http://dx.doi.org/10.1093/bbb/zbab070.

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ABSTRACT The ribosome requires metal ions for structural stability and translational activity. These metal ions are important for stabilizing the secondary structure of ribosomal RNA, binding of ribosomal proteins to the ribosome, and for interaction of ribosomal subunits. In this review, various relationships between ribosomes and metal ions, especially Mg2+ and Zn2+, are presented. Mg2+ regulates gene expression by modulating the translational stability and synthesis of ribosomes, which in turn contribute to the cellular homeostasis of Mg2+. In addition, Mg2+ can partly complement the function of ribosomal proteins. Conversely, a reduction in the cellular concentration of Zn2+ induces replacement of ribosomal proteins, which mobilizes free-Zn2+ in the cell and represses translation activity. Evolutional relationships between these metal ions and the ribosome are also discussed.
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Sulima and Dinman. "The Expanding Riboverse." Cells 8, no. 10 (October 5, 2019): 1205. http://dx.doi.org/10.3390/cells8101205.

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Subverting the conventional concept of “the” ribosome, a wealth of information gleaned from recent studies is revealing a much more diverse and dynamic ribosomal reality than has traditionally been thought possible. A diverse array of researchers is collectively illuminating a universe of heterogeneous and adaptable ribosomes harboring differences in composition and regulatory capacity: These differences enable specialization. The expanding universe of ribosomes not only comprises an incredible richness in ribosomal specialization between species, but also within the same tissues and even cells. In this review, we discuss ribosomal heterogeneity and speculate how the emerging understanding of the ribosomal repertoire is impacting the biological sciences today. Targeting pathogen-specific and pathological “diseased” ribosomes promises to provide new treatment options for patients, and potential applications for “designer ribosomes” are within reach. Our deepening understanding of and ability to manipulate the ribosome are establishing both the technological and theoretical foundations for major advances for the 21st century and beyond.
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Guth-Metzler, Rebecca, Marcus S. Bray, Moran Frenkel-Pinter, Suttipong Suttapitugsakul, Claudia Montllor-Albalate, Jessica C. Bowman, Ronghu Wu, et al. "Cutting in-line with iron: ribosomal function and non-oxidative RNA cleavage." Nucleic Acids Research 48, no. 15 (July 14, 2020): 8663–74. http://dx.doi.org/10.1093/nar/gkaa586.

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Abstract Divalent metal cations are essential to the structure and function of the ribosome. Previous characterizations of the ribosome performed under standard laboratory conditions have implicated Mg2+ as a primary mediator of ribosomal structure and function. Possible contributions of Fe2+ as a ribosomal cofactor have been largely overlooked, despite the ribosome's early evolution in a high Fe2+ environment, and the continued use of Fe2+ by obligate anaerobes inhabiting high Fe2+ niches. Here, we show that (i) Fe2+ cleaves RNA by in-line cleavage, a non-oxidative mechanism that has not previously been shown experimentally for this metal, (ii) the first-order in-line rate constant with respect to divalent cations is >200 times greater with Fe2+ than with Mg2+, (iii) functional ribosomes are associated with Fe2+ after purification from cells grown under low O2 and high Fe2+ and (iv) a small fraction of Fe2+ that is associated with the ribosome is not exchangeable with surrounding divalent cations, presumably because those ions are tightly coordinated by rRNA and deeply buried in the ribosome. In total, these results expand the ancient role of iron in biochemistry and highlight a possible new mechanism of iron toxicity.
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Jiang, M., S. M. Sullivan, A. K. Walker, J. R. Strahler, P. C. Andrews, and J. R. Maddock. "Identification of Novel Escherichia coli Ribosome-Associated Proteins Using Isobaric Tags and Multidimensional Protein Identification Techniques." Journal of Bacteriology 189, no. 9 (March 2, 2007): 3434–44. http://dx.doi.org/10.1128/jb.00090-07.

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ABSTRACT Biogenesis of the large ribosomal subunit requires the coordinate assembly of two rRNAs and 33 ribosomal proteins. In vivo, additional ribosome assembly factors, such as helicases, GTPases, pseudouridine synthetases, and methyltransferases, are also critical for ribosome assembly. To identify novel ribosome-associated proteins, we used a proteomic approach (isotope tagging for relative and absolute quantitation) that allows for semiquantitation of proteins from complex protein mixtures. Ribosomal subunits were separated by sucrose density centrifugation, and the relevant fractions were pooled and analyzed. The utility and reproducibility of the technique were validated via a double duplex labeling method. Next, we examined proteins from 30S, 50S, and translating ribosomes isolated at both 16°C and 37°C. We show that the use of isobaric tags to quantify proteins from these particles is an excellent predictor of the particles with which the proteins associate. Moreover, in addition to bona fide ribosomal proteins, additional proteins that comigrated with different ribosomal particles were detected, including both known ribosomal assembly factors and unknown proteins. The ribosome association of several of these proteins, as well as others predicted to be associated with ribosomes, was verified by immunoblotting. Curiously, deletion mutants for the majority of these ribosome-associated proteins had little effect on cell growth or on the polyribosome profiles.
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Yang, Rui, Luis R. Cruz-Vera, and Charles Yanofsky. "23S rRNA Nucleotides in the Peptidyl Transferase Center Are Essential for Tryptophanase Operon Induction." Journal of Bacteriology 191, no. 11 (March 27, 2009): 3445–50. http://dx.doi.org/10.1128/jb.00096-09.

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ABSTRACT Distinct features of the ribosomal peptide exit tunnel are known to be essential for recognition of specific amino acids of a nascent peptidyl-tRNA. Thus, a tryptophan residue at position 12 of the peptidyl-tRNA TnaC-tRNAPro leads to the creation of a free tryptophan binding site within the ribosome at which bound tryptophan inhibits normal ribosome functions. The ribosomal processes that are inhibited are hydrolysis of TnaC-tRNAPro by release factor 2 and peptidyl transfer of TnaC of TnaC-tRNAPro to puromycin. These events are normally performed in the ribosomal peptidyl transferase center. In the present study, changes of 23S rRNA nucleotides in the 2585 region of the peptidyl transferase center, G2583A and U2584C, were observed to reduce maximum induction of tna operon expression by tryptophan in vivo without affecting the concentration of tryptophan necessary to obtain 50% induction. The growth rate of strains with ribosomes with either of these changes was not altered appreciably. In vitro analyses with mutant ribosomes with these changes showed that tryptophan was not as efficient in protecting TnaC-tRNAPro from puromycin action as wild-type ribosomes. However, added tryptophan did prevent sparsomycin action as it normally does with wild-type ribosomes. These findings suggest that these two mutational changes act by reducing the ability of ribosome-bound tryptophan to inhibit peptidyl transferase activity rather than by reducing the ability of the ribosome to bind tryptophan. Thus, the present study identifies specific nucleotides within the ribosomal peptidyl transferase center that appear to be essential for effective tryptophan induction of tna operon expression.
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Mandon, Elisabet C., Ying Jiang, and Reid Gilmore. "Dual recognition of the ribosome and the signal recognition particle by the SRP receptor during protein targeting to the endoplasmic reticulum." Journal of Cell Biology 162, no. 4 (August 11, 2003): 575–85. http://dx.doi.org/10.1083/jcb.200303143.

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We have analyzed the interactions between the signal recognition particle (SRP), the SRP receptor (SR), and the ribosome using GTPase assays, biosensor experiments, and ribosome binding assays. Possible mechanisms that could contribute to an enhanced affinity between the SR and the SRP–ribosome nascent chain complex to promote protein translocation under physiological ionic strength conditions have been explored. Ribosomes or 60S large ribosomal subunits activate the GTPase cycle of SRP54 and SRα by providing a platform for assembly of the SRP–SR complex. Biosensor experiments revealed high-affinity, saturable binding of ribosomes or large ribosomal subunits to the SR. Remarkably, the SR has a 100-fold higher affinity for the ribosome than for SRP. Proteoliposomes that contain the SR bind nontranslating ribosomes with an affinity comparable to that shown by the Sec61 complex. An NH2-terminal 319-residue segment of SRα is necessary and sufficient for binding of SR to the ribosome. We propose that the ribosome–SR interaction accelerates targeting of the ribosome nascent chain complex to the RER, while the SRP–SR interaction is crucial for maintaining the fidelity of the targeting reaction.
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Kazibwe, Zakayo, Ang-Yu Liu, Gustavo C. MacIntosh, and Diane C. Bassham. "The Ins and Outs of Autophagic Ribosome Turnover." Cells 8, no. 12 (December 10, 2019): 1603. http://dx.doi.org/10.3390/cells8121603.

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Ribosomes are essential for protein synthesis in all organisms and their biogenesis and number are tightly controlled to maintain homeostasis in changing environmental conditions. While ribosome assembly and quality control mechanisms have been extensively studied, our understanding of ribosome degradation is limited. In yeast or animal cells, ribosomes are degraded after transfer into the vacuole or lysosome by ribophagy or nonselective autophagy, and ribosomal RNA can also be transferred directly across the lysosomal membrane by RNautophagy. In plants, ribosomal RNA is degraded by the vacuolar T2 ribonuclease RNS2 after transport by autophagy-related mechanisms, although it is unknown if a selective ribophagy pathway exists in plants. In this review, we describe mechanisms of turnover of ribosomal components in animals and yeast, and, then, discuss potential pathways for degradation of ribosomal RNA and protein within the vacuole in plants.
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Pecoraro, Annalisa, Martina Pagano, Giulia Russo, and Annapina Russo. "Ribosome Biogenesis and Cancer: Overview on Ribosomal Proteins." International Journal of Molecular Sciences 22, no. 11 (May 23, 2021): 5496. http://dx.doi.org/10.3390/ijms22115496.

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Cytosolic ribosomes (cytoribosomes) are macromolecular ribonucleoprotein complexes that are assembled from ribosomal RNA and ribosomal proteins, which are essential for protein biosynthesis. Mitochondrial ribosomes (mitoribosomes) perform translation of the proteins essential for the oxidative phosphorylation system. The biogenesis of cytoribosomes and mitoribosomes includes ribosomal RNA processing, modification and binding to ribosomal proteins and is assisted by numerous biogenesis factors. This is a major energy-consuming process in the cell and, therefore, is highly coordinated and sensitive to several cellular stressors. In mitochondria, the regulation of mitoribosome biogenesis is essential for cellular respiration, a process linked to cell growth and proliferation. This review briefly overviews the key stages of cytosolic and mitochondrial ribosome biogenesis; summarizes the main steps of ribosome biogenesis alterations occurring during tumorigenesis, highlighting the changes in the expression level of cytosolic ribosomal proteins (CRPs) and mitochondrial ribosomal proteins (MRPs) in different types of tumors; focuses on the currently available information regarding the extra-ribosomal functions of CRPs and MRPs correlated to cancer; and discusses the role of CRPs and MRPs as biomarkers and/or molecular targets in cancer treatment.
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Ghulam, Mustafa Malik, Mathieu Catala, and Sherif Abou Elela. "Differential expression of duplicated ribosomal protein genes modifies ribosome composition in response to stress." Nucleic Acids Research 48, no. 4 (December 21, 2019): 1954–68. http://dx.doi.org/10.1093/nar/gkz1183.

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Abstract In Saccharomyces cerevisiae, most ribosomal proteins are synthesized from duplicated genes, increasing the potential for ribosome heterogeneity. However, the contribution of these duplicated genes to ribosome production and the mechanism determining their relative expression remain unclear. Here we demonstrate that in most cases, one of the two gene copies generate the bulk of the active ribosomes under normal growth conditions, while the other copy is favored only under stress. To understand the origin of these differences in paralog expression and their contribution to ribosome heterogeneity we used RNA polymerase II ChIP-Seq, RNA-seq, polyribosome association and peptide-based mass-spectrometry to compare their transcription potential, splicing, mRNA abundance, translation potential, protein abundance and incorporation into ribosomes. In normal conditions a post-transcriptional expression hierarchy of the duplicated ribosomal protein genes is the product of the efficient splicing, high stability and efficient translation of the major paralog mRNA. Exposure of the cell to stress modifies the expression ratio of the paralogs by repressing the expression of the major paralog and thus increasing the number of ribosomes carrying the minor paralog. Together the data indicate that duplicated ribosomal protein genes underlie a modular network permitting the modification of ribosome composition in response to changing growth conditions.
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Dissertations / Theses on the topic "Ribosomas"

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Rivero, Jiménez Matías Alberto. "Estudio del mecanismo de inicio de la traducción del mensajero completo del virus de la inmunodeficiencia humana de tipo 1 : caracterización de un modelo de iniciación dual." Tesis, Universidad de Chile, 2011. http://repositorio.uchile.cl/handle/2250/105392.

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En organismos eucariontes, el inicio de la síntesis de proteínas comienza con el reclutamiento de la subunidad 40S del ribosoma al mRNA. Sin embargo, dependiendo de cómo se efectúe este reclutamiento, el inicio de la traducción puede ser dependiente o independiente de la estructura 5’cap. El mecanismo cap-dependiente se basa en el reconocimiento de la estructura cap (7mGpppN), presente en el extremo 5’ de todos los mRNA, por el complejo de iniciación eIF4F. El complejo eIF4F está constituido por tres proteínas: eIF4E, la proteína de unión al cap; eIF4A, una RNA helicasa ATP dependiente y la proteína de andamiaje, eIF4G. La subunidad 40S ribosomal es reclutada al mRNA como parte de un complejo formado por eIF2-GTP/Met-tRNAi, eIF1A y eIF3. El factor de iniciación eIF4G cumple la función de proteína puente entre la subunidad 40S del ribosoma (vía eIF3) y el mRNA (vía eIF4E). Luego del reclutamiento de la subunidad 40S ribosomal en la vecindad de la estructura cap, el complejo de iniciación migra en dirección 5’ a 3’ hasta encontrar un codón de inicio de la síntesis de proteína, AUG, en un contexto óptimo. El estudio del mecanismo de traducción de los mRNA de la familia Picornaviridae, los cuales carecen de estructura 5’cap, permitió la caracterización de un mecanismo alternativo de iniciación de la síntesis de proteína. El mecanismo de inicio de la traducción en los mRNA de Picornavirus está mediado por regiones de RNA altamente estructuradas que son capaces de reclutar la subunidad 40S ribosomal de manera independiente a los extremos del mRNA. Estas estructuras de RNA se denominaron sitios internos de entrada de ribosomas, IRES (por sus siglas en inglés). Desde su caracterización inicial en los mRNA de la familia Picornaviridae, la existencia de IRES se ha extendido a otras familias virales incluyendo a la familia Retroviridae. El virus de la inmunodeficiencia humana de tipo 1 (VIH-1) pertenece al género Lentivirus de la familia Retroviridae. El genoma de VIH-1 está constituido por dos hebras idénticas de un RNA de cadena simple de polaridad positiva, unidas entre si por enlaces no covalentes. El mRNA de VIH-1 posee cap, 3’poli(A) y dos elementos IRES, el primero, IRES-1, en su región 5’ no traducida (5’UTR) y el segundo en su región codificante para la proteína viral Gag (IRES-40K). Este trabajo se focalizó en el estudio de la función del IRES-1 de VIH-1 partiendo del postulado que a diferencia de otros mRNAs virales que poseen un elemento IRES, y sólo pueden iniciar la traducción de manera IRES dependiente, el mRNA de VIH-1 posee la capacidad de iniciar la síntesis de proteína de manera dual, es decir, de manera dependiente y/o independiente de la estructura cap. Este trabajo establece que el mRNA completo de VIH-1 puede iniciar su traducción utilizando un mecanismo tanto dependiente como independiente de su estructura 5’cap. En este contexto se establece que el mRNA de VIH-1 comparte características funcionales descritas sólo para mRNA celulares, diferenciándose de manera importante de los otros mRNA virales que poseen un elemento IRES que inician su traducción exclusivamente de manera dependiente de IRES.
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Morcelle, Magaña Carmen. "The role of the RPL5/RPL11/5S rRNA complex in mediating p53 levels in response to c-Myc depletion in colorectal carcinoma." Doctoral thesis, Universitat de Barcelona, 2017. http://hdl.handle.net/10803/457876.

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In most human cancers, the c-Myc transcription factor is deregulated and/or its levels are elevated, particularly in colorectal cancer (CRC). Earlier studies suggested a direct relationship between ribosome biogenesis and c-Myc-induced tumorigenesis, with recent reports arguing that ribosomal proteins L5 (RPL5) and RPL11 act against c- Myc-driven tumorigenesis as tumor suppressors by inhibiting MDM2 and inducing p53 stabilization. Our laboratory recently showed that upon inhibition of ribosome biogenesis, a nascent pre-ribosomal complex containing RPL5, RPL11 and 5S rRNA is redirected from 60S ribosome biogenesis to the inhibition of MDM2 and p53 stabilization. We have termed this response the impaired ribosome biogenesis checkpoint (IRBC). Here, we demonstrate that c-Myc silencing causes a drop in p53 protein levels through increased proteasome degradation. Moreover, c-Myc depletion significantly reduces the levels of the RPL5/RPL11/5S rRNA complex, even following impaired ribosome biogenesis by treatment with Actinomycin D, a RNA polymerase I inhibitor. Thus, diminished p53 stability appears to be mediated by a reduction of the RPL5/RPL11/5S rRNA complex and a decrease of the inhibition of MDM2. This thesis examines the relationship between c-Myc, p53 and components of the IRBC complex, including the 5S rRNA, defining a mechanism by which cells respond to c-Myc levels.
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Meza, Soto Stfanny Wendy. "Estudio preliminar de la interacción entre la proteína del síndrome de Werner, presente en la fracción citoplasmática de células HeLa, y la proteína ribosomal humana S3 recombinante mediante el ensayo in vitro de pull-down." Bachelor's thesis, Universidad Nacional Mayor de San Marcos, 2018. https://hdl.handle.net/20.500.12672/8314.

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El gen WRN codifica a la proteína del síndrome de Werner (WRN), una proteína multifuncional con actividad helicasa y exonucleasa. Datos previos indican que WRN está asociada a la maquinaria traduccional y relacionada con las vías metabólicas que regulan la síntesis de macromoléculas, la producción de energía y el balance de óxidoreducción (redox) implicados en la proliferación celular. La proteína ribosomal eucariota S3 (eRPS3) es un elemento importante de la subunidad ribosomal menor 40S que promueve el reconocimiento del codón de inicio y la interacción con el ácido ribonucleico mensajero (ARNm) para el desarrollo de la síntesis proteica. La asociación entre la proteína ribosomal humana S3 (hRPS3) y WRN ha sido descrita previamente mediante ensayos de co-inmunoprecipitación, inmunoprecipitación y pulldown usando extractos totales de células embrionarias de riñón. Se identifica la interacción entre WRN, presente en la fracción citoplasmática de células HeLa, y la hRPS3. Mediante el uso de la tecnología de ADN recombinante se sintetizó en E. coli la proteína hRPS3 fusionada a una cola de seis histidinas (hRPS3-6xHis). Esta proteína de fusión fue inmovilizada por cromatografía de afinidad en una resina de agarosa con iones níquel, y se usó conjuntamente con la fracción citoplasmática de células HeLa que contenía a WRN para llevar a cabo el ensayo de pull-down. El análisis por Western blot del pull-down evidenció la presencia de WRN en la resina que contenía a la proteína de fusión hRPS3-6xHis. Este resultado demuestra la interacción entre WRN presente en el citoplasma y la hRPS3 que es un elemento importante de la maquinaria de traducción.
Tesis
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Adriano, Escobar Gina Jackelinne. "Caracterización molecular de bacterias celulolíticas aisladas de ambientes salinos del Perú." Bachelor's thesis, Universidad Nacional Mayor de San Marcos, 2012. https://hdl.handle.net/20.500.12672/12154.

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Identifica las bacterias celulolíticas productoras de celulasas extracelulares aisladas de ambientes salinos de Perú. Para ello, se utilizaron 140 aislados, 25 de Maras (Cusco), 28 de Chilca (Lima), 42 de Pilluana (San Martín), 25 de San Blas (Junín) y 20 de la bahía de Paracas (Ica), todos fueron sembrados en agar carboximeti lcelulosa 1 % (p/v) suplementado con extracto de levadura 0,5 % y agua de sales 5%, se incubaron a 37 °C durante 48 h, luego se añadió a las placas solución rojo de congo 1 % (p/v) como agente revelador. Se seleccionaron 20 bacterias con actividad celulolítica, que se caracterizaron en base a pruebas morfológicas, bioquímicas y nutricionales. El análisis de restricción de los genes ribosómicos 16S amplificados por la reacción en cadena de la polimerasa se empleó para analizar la diversidad genética de los aislados productores de celulasas, del cual se obtuvieron 8 genotipos diferentes. Se secuenciaron los genes ribosómicos 16S de las cepas CHR3, CH48, CONT1 y PAR6R01A, las cuales presentaron la mayor actividad celulolítica. Del análisis de las secuencias nucleotídicas se determinó que estas cepas están relacionadas con Staphylococcus cohnii, Bacillus saferensis, Halomonas elongata y Halomonas sp, respectivamente.
Tesis
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Gallo, López Carolina 1984. "Determinants of growth rate in genome-reduced bacteria." Doctoral thesis, Universitat Pompeu Fabra, 2018. http://hdl.handle.net/10803/664510.

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Understanding how the growth rate is regulated in bacteria is an ongoing challenge in biology and its controlled regulation would have a great impact in the biotechnological industry. Growth rates may be regulated by several genetic factors, but despite some of them are known, we are still unable to rationally increase bacterial growth rates. Most studies are done in fast-growing and highly complex bacteria with large and redundant genomes. Mycoplasma pneumoniae, from the Mollicutes class, is a simpler organism with one of the smallest genomes. Furthermore, Mollicutes species have wide range of growth rates and reduced genomes making them appealing for growth studies. In this thesis, we investigated the genetic determinants of growth rates in M. pneumoniae and in other Mollicutes species by different approaches. Our results corroborated some genetic factors reported to be associated to fast growth and found additional translational and metabolic determinants that have not been described before.
Entender cómo se regula la tasa de crecimiento en bacterias es uno de los retos en curso en biología y su regulación controlada tendría un gran impacto en la industria biotecnológica. Las tasas de crecimiento pueden ser reguladas por varios factores genéticos, pero a pesar de que algunos de ellos son en parte conocidos, aún somos incapaces de incrementar las tasas de crecimiento racionalmente. La mayoría de estudios se han llevado a cabo en bacterias de crecimiento rápido y complejas con genomas grandes y redundantes. Mycoplasma pneumoniae, de la clase Mollicutes, es un organismo más simple con uno de los genomas más pequeño y con poca redundancia. Adicionalmente, las especies de Mollicutes tienen un amplio rango de tasas de crecimiento y genomas reducidos, lo cual las hace atractivas para estudios de crecimiento. En esta tesis, investigamos los determinantes genéticos de las tasas de crecimiento en M. pneumoniae y en otras especies de Mollicutes por medio de enfoques diferentes. Nuestros resultados corroboraron algunos de los ya reportados factores genéticos asociados a un crecimiento rápido y encontramos además determinantes traduccionales y metabólicos que no habían sido descritos anteriormente.
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Domostegui, Fernández Ana. "IRBC-induced p53-dependent Cell Death in c-MYC-driven tumors mediated by loss of MCL1." Doctoral thesis, Universitat de Barcelona, 2019. http://hdl.handle.net/10803/668147.

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The oncogene MYC is altered and its expression is deregulated in up to 70% of human cancers, including B cell neoplasms. Earlier studies in a mouse model of Eμ-MYC-driven B-cell lymphomas reported that oncogenic MYC relies on aberrant rates of ribosome biogenesis (RiBi) and protein synthesis to sustain rapid growth and proliferation of B-cell lymphomas. As MYC driven B-cell lymphomas are addicted to hyperactivation of RiBi, it has emerged as a potential clinical target. However, it is unclear whether targeting RiBi induces regression of MYC-driven tumors by decreasing translational capacity and/or by inducing the impaired ribosome biogenesis checkpoint (IRBC), leading to p53 stabilization. We set to address this question by generating an inducible system in Eμ-MYC-driven lymphoma cells to deplete either one of two essential 60S ribosomal proteins (RPs), RPL7a or RPL11, the latter a component of the IRBC complex. Depletion of either RP mRNA by ~50% had an equivalent impact on RiBi, protein synthesis and cell growth, however only depletion of RPL7a led to the induction of the IRBC, p53 stabilization, and acute induction of apoptosis. Importantly, we observed that this response is driven by the selective degradation of the antiapoptotic form of MCL1, of the BCL2 family, whose overexpression is critical to sustain survival and growth of Eμ-MYC lymphomas. MCL1 is commonly overexpressed in many human cancers, especially in B cell malignancies, is frequently found co-amplified with MYC, and its overexpression is associated with bad prognosis, resistance to therapy and relapse. Despite the tremendous investment in the development of selective MCL1 inhibitors in the clinic, we show that nanomolar concentrations Actinomycin D (ActD), an FDA approved drug for particular types of cancer, specifically disrupts the synthesis of rRNA and RiBi, leading to IRBC activation, p53 stabilization and degradation of the antiapoptotic form of MCL1, and killing Trp53+/+, but not Trp53-/- Eμ-MYC lymphoma cells. Finally, we provide preclinical data that mice bearing Trp53+/+, but not Trp53-/-, Eμ-MYC lymphomas are exquisitely protected from lymphomagenesis by ActD. Therefore, in MYC-driven tumors, the IRBC elicits p53-dependent apoptosis, which is mediated by the loss of the antiapoptotic form of MCL1.
La expresión del oncogen MYC está desregulada en hasta un 70% de los cánceres humanos, incluyendo los neoplasmas de células B. Estudios previos en el modelo murino de linfoma de células B Eμ-MYC demostraron que la expresión oncogénica de MYC requiere de tasas de biogénesis de ribosomas (RiBi) y síntesis de proteínas aberrantes para el rápido crecimiento y proliferación de estos tumores y que son adictos a la hiperactivación de la RiBi, convirtiéndose en una potencial diana terapéutica. Sin embargo, si inhibir la RiBi promueve la regresión tumoral mediante la disminución de la capacidad de traducción y/o por la inducción del punto de control de daño en la biogénesis de ribosomas (IRBC) y la consiguiente estabilización de p53, no está claro. Para resolver esta controversia, generamos un sistema inducible que elimina la proteína ribosomal (RP)L7a o la RPL11 en células Eμ-MYC, las dos constituyentes del ribosoma 60S, pero la última esencial del complejo IRBC. Una reducción del 50% en el mRNA de cualquiera de las dos tiene un impacto similar en la RiBi, la síntesis de proteínas y el crecimiento celular; pero sólo la reducción de la RPL7a induce el IRBC, estabiliza p53 e induce apoptosis. Además, esta respuesta se desencadena mediante la degradación selectiva de la forma antiapoptótica de MCL1, cuya sobreexpresión es crucial para la supervivencia y el crecimiento de los linfomas Eμ-MYC. MCL1 se sobreexpresa en muchos tumores, especialmente en los de células B, frecuentemente co- amplifica con MYC y se asocia a peor prognosis, resistencia y recaída. A pesar de la tremenda inversión en el desarrollo de inhibidores selectivos de MCL1 en la clínica, nosotros demostramos que concentraciones nanomolares de Actinomicina D (ActD), fármaco aprobado por la FDA para tratar ciertos tumores, interrumpe selectivamente la síntesis de rRNA y la RiBi, activa el IRBC, estabiliza p53 y degrada específicamente la forma antiapoptótica de MCL1, acabando con las células de linfoma Eμ-MYC Trp53+/+ pero no con aquellas Trp53-/-. Finalmente, proporcionamos datos preclínicos en los que la ActD protege contra la linfomagénesis a ratones transplantados con linfomas Eμ-MYC Trp53+/+ pero no con linfomas Eμ-MYC Trp53-/-. Por tanto, en estos tumores dirigidos por MYC, el IRBC activa apoptosis por p53, la cual requiere de la degradación de la forma antiapoptótica de MCL1.
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Shimmin, Lawrence Charles. "An archaebacterial ribosomal protein gene cluster." Thesis, University of British Columbia, 1990. http://hdl.handle.net/2429/30994.

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The eubacteria, archaebacteria and eucaryota evolved from a common ancestral state, the progenote, approximately 4,000 million years ago. The archaebacteria flourish in extreme environments, exhibiting unusual macromolecular structures and metabolism of which much has recently been elucidated. Less, however, is known of the genetics of archaebacteria. In order to investigate gene structure, organization, regulation and evolution in the archaebacteria a gene cluster encoding the ribosomal proteins of the GTPase domain was cloned from the extremely halophilic archaebacterium Halobacterium cutirubrum, characterized and compared with the homologous genes and proteins from eubacteria and eucaryota. A clone containing a 5146 basepair insert of genomic Halobacterium cutirubrum NRCC 34001 DNA encoding the GTPase domain ribosomal proteins was characterized and discovered to retain the identical gene order (i.e. L11e, Lie, L10e and L12e) as the homologous Escherichia coli genes and in addition two transcribed upstream open reading frames encoding the potential proteins ORF, of unknown function and NAB, bearing sequence similarity to nucleic acid binding proteins. The predominant transcripts are monocistronic L11e and tricistronic Lie - L10e - L12e transcripts; monocistronic NAB and bicistronic NAB - L11e transcripts are present at reduced levels and the ORF is present as a very rare transcript. Common elements upstream of the transcription initiation sites include the motif TTCGA ... 4-15 bp ... TTAA ... 20-26 bp ... A or G transcription start. The NAB and some of the ORF transcripts are divergently transcribed from a single TTAA promotor element. The NAB and some of the ORF transcripts initiate 1 nucleotide before the coding region; the L11e monocistronic transcript initiates precisely at the first A of the initiator methionine ATG codon. The Lie - L10e - L12e tricistronic transcript has a 75 nucleotide leader that is probably involved in the autogenous regulation of the transcript at the translational level by the Lie protein. Termination of transcription occurs, with a single exception, within T tracts after GC rich regions. Although classic Shine-Dalgarno (eubacterial) type ribosome binding sites are present upstream of the Lie and L10e genes, the mechanism of translation initiation for transcripts with nil or negligible 5' leaders remains to be elucidated. Alignments between the deduced amino acid sequences of the L1le, Lie, Ll0e and L12eribosomal proteins and other available homologous proteins of archaebacteria, eubacteria and eucaryota have been made and show that the L11e, Lie and L10e proteins are colinear whereas the L12e protein has suffered a rearrangement through what appears to be gene fusion events. The L11e proteins exhibit (i) sequence conservation in the region interacting with release factor 1, (ii) conserved proline residues (probably contributing to the elongated shape of the molecule) and (iii) sites of methylation in Eco L11 are not conserved in the archaebacterial L11e proteins. The Lie proteins have regions of very high sequence similarity near the center and carboxy termini of the proteins but the relationships between protein structure and function remain unknown. Intraspecies comparisons between L10e and L12e sequences indicate the archaebacterial and eucaryotic L10e proteins contain a partial copy of the L12e protein fused to their carboxy terminus. In the eubacteria most of this fusion has been removed by a carboxy terminal deletion. Within the L12e derived region a 26 amino acid long internal modular sequence reiterated thrice in the archaebacterial L10e, twice in the eucaryotic L10e and once in the eubacterial L10e was discovered. This modular sequence also appears to be present in single copy in all Ll2e proteins and may play a role in L12e dimerization, L10e - L12e complex formation and the function of L10e - L12e complex in translation. From these sequence comparisons a model depicting the evolutionary progression gene cluster and proteins from the primordial state to the contemporary archaebacterial, eucaryotic and eubacterial states is presented.
Medicine, Faculty of
Biochemistry and Molecular Biology, Department of
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Dator, Romel P. "Characterization of Ribosomes and Ribosome Assembly Complexes by Mass Spectrometry." University of Cincinnati / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1382373082.

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Roy, Poorna. "Deconstructing the ribosome: specific interactions of a ribosomal RNA fragment with intact and fragmented L23 ribosomal protein." Thesis, Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/47579.

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The complexity of translation is a classical dilemma in the evolution of biological systems. Efficient translation requires coordination of complex, highly evolved RNAs and proteins; however, complex, highly evolved RNAs and proteins could not evolve without efficient translation system. At the heart of this complexity is the ribosome, itself a remarkably complex molecular machine. Our work illustrates the ribosome as deconstructed units of modification. Here we have deconstructed a segment of the ribosome to interacting RNA-protein units. L23 interacts in vivo with both Domain III (DIII) and Domain IIIcore (DIIIcore) independently of the fully assembled ribosome. This suggests that DIIIcore represents the functional rRNA unit in DIII-L23 interaction. Furthermore, L23peptide sustains binding function in vitro with both DIII and DIIIcore independently of any stabilizing effects from the globular domain of L23. The ability of L23peptide to form a 1:1 complex with both DIII and DIIIcore suggests that L23peptide is the functional rProtein unit in DIII-L23 interaction. We believe that our results will stimulate interest and discussions in the significance of 3D architecture and units of evolution in the ribosome. The ubiquity of the ribosome in cellular life prognosticates that our results impact and appeal to biologists, chemists, bioinformaticists, as well as the general scientific community.
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Riaño, Canalias Ferran. "The effect of inhibition of nucleotide synthesis on ribosome biogenesis and the induction of p53." Doctoral thesis, Universitat de Barcelona, 2017. http://hdl.handle.net/10803/457972.

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Ribosome biogenesis is one of the most energy consuming anabolic processes in a cell, required for the generation of the translational machinery to grow and proliferate. Moreover, this process necessitates the coordination of protein and nucleotide synthesis to generate ribosomal proteins (RPs) and ribosomal RNA (rRNA). Critically, increased rates of ribosome biogenesis are a hallmark of c-Myc driven CRC required to sustain exacerbated growth and proliferation, with recent studies showing that drugs that target ribosome biogenesis are clinically efficacious. We have previously shown that upon ribosome biogenesis impairment, a pre‐ribosomal complex formed by RPL11 and RPL5 and noncoding 5S rRNA is re‐directed from the incorporation into the pre-60S ribosome, to bind and inhibit HDM2, leading to p53 stabilization and cell cycle arrest. We have termed this response the Impaired Ribosome Biogenesis Checkpoint (IRBC). In this study I set out to analyze the effect of nucleotide depletion on ribosome biogenesis in c-Myc-driven CRC cell lines, addressing the role of the IRBC. Nucleotide depletion inhibited rRNA synthesis and elicited the IRBC, p53 stabilization, but failed to induce G1 cell cycle arrest as previously reported. I found that this was due to the loss of 5S RNA production, the limiting factor in triggering the IRBC, causing a disruption of the IRBC complex. Moreover, this allowed cells to escape G1 arrest and enter S phase, where they encountered replicative stress. These data support the hypothesis that in nucleotide deprived conditions the IRBC acts to hold cells in G1 to prevent them from replicating their DNA cells and eventually encountering genomic instability.
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Books on the topic "Ribosomas"

1

Rodnina, Marina V., Wolfgang Wintermeyer, and Rachel Green. Ribosomes: Structure, function, and dynamics. Edited by Ribosomes Meeting (2010 : Orvieto, Italy). Wien: Springer, 2011.

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Romero-Zepeda, Hilda. The influence of ribosomal proteins on the action of ribosome-inactivating proteins. [s.l.]: typescript, 1999.

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Spirin, A. S. Ribosomes. New York: Kluwer Academic/Plenum Publishers, 1999.

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Ribosomes. New York: Kluwer Academic/Plenum, 1999.

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Rodnina, Marina V., Wolfgang Wintermeyer, and Rachel Green, eds. Ribosomes. Vienna: Springer Vienna, 2011. http://dx.doi.org/10.1007/978-3-7091-0215-2.

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Spirin, Alexander S. Ribosomes. Boston, MA: Springer US, 1999. http://dx.doi.org/10.1007/978-1-4615-7817-8.

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Lake, James A. The ribosome. [Preston: Lancashire Polytechnic.Library and Learning Resources Service, 1988.

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Garrett, Roger A., ed. The Ribosome. Washington, DC, USA: ASM Press, 2000. http://dx.doi.org/10.1128/9781555818142.

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Labunskyy, Vyacheslav M., ed. Ribosome Profiling. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1150-0.

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Stirpe, Fiorenzo, and Douglas A. Lappi, eds. Ribosome-inactivating Proteins. Oxford: John Wiley & Sons, Ltd., 2014. http://dx.doi.org/10.1002/9781118847237.

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Book chapters on the topic "Ribosomas"

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Vainshtein, B. K., and S. D. Trakhanov. "Crystallization of Ribosomes, Ribosomal Subunits, and Individual Ribosomal Proteins." In Growth of Crystals, 169–80. Boston, MA: Springer US, 1991. http://dx.doi.org/10.1007/978-1-4615-3662-8_12.

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Kitahara, Kei, and Kentaro Miyazaki. "Constructing Mutant Ribosomes Containing Mutant Ribosomal RNAs." In Applied RNA Bioscience, 17–32. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-10-8372-3_2.

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Spirin, Alexander S. "Elongation Cycle, Step III: Translocation." In Ribosomes, 213–39. Boston, MA: Springer US, 1999. http://dx.doi.org/10.1007/978-1-4615-7817-8_12.

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Spirin, Alexander S. "Protein Biosynthesis." In Ribosomes, 3–5. Boston, MA: Springer US, 1999. http://dx.doi.org/10.1007/978-1-4615-7817-8_1.

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Spirin, Alexander S. "Elongation Cycle, Step I: Aminoacyl-tRNA Binding." In Ribosomes, 163–93. Boston, MA: Springer US, 1999. http://dx.doi.org/10.1007/978-1-4615-7817-8_10.

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Spirin, Alexander S. "Elongation Cycle, Step II: Transpeptidation (Peptide Bond Formation)." In Ribosomes, 195–211. Boston, MA: Springer US, 1999. http://dx.doi.org/10.1007/978-1-4615-7817-8_11.

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Spirin, Alexander S. "Elongation Rate and its Modulation." In Ribosomes, 241–59. Boston, MA: Springer US, 1999. http://dx.doi.org/10.1007/978-1-4615-7817-8_13.

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Spirin, Alexander S. "Termination of Translation." In Ribosomes, 261–70. Boston, MA: Springer US, 1999. http://dx.doi.org/10.1007/978-1-4615-7817-8_14.

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Spirin, Alexander S. "Initiation of Translation." In Ribosomes, 271–308. Boston, MA: Springer US, 1999. http://dx.doi.org/10.1007/978-1-4615-7817-8_15.

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Spirin, Alexander S. "Translational Control in Prokaryotes." In Ribosomes, 309–38. Boston, MA: Springer US, 1999. http://dx.doi.org/10.1007/978-1-4615-7817-8_16.

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Conference papers on the topic "Ribosomas"

1

Fox, George E., Maxim Paci, Quyen Tran, Anton S. Petrov, and Loren D. Williams. "Ribosome dynamics and the evolutionary history of ribosomes." In SPIE Optical Engineering + Applications, edited by Richard B. Hoover, Gilbert V. Levin, Alexei Yu Rozanov, and Nalin C. Wickramasinghe. SPIE, 2015. http://dx.doi.org/10.1117/12.2187098.

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Chatterjee, Pratima, Mayukh Sarkar, and Prasun Ghosal. "Computing in Ribosomes: Performing Boolean Logic Using mRNA-Ribosome System." In 2016 IEEE Computer Society Annual Symposium on VLSI (ISVLSI). IEEE, 2016. http://dx.doi.org/10.1109/isvlsi.2016.128.

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Chatterjee, Pratima, Mayukh Sarkar, and Prasun Ghosal. "Computing in Ribosomes: Implementing Sequential Circuits Using mRNA-Ribosome System." In 2016 IEEE International Symposium on Nanoelectronic and Information Systems (iNIS). IEEE, 2016. http://dx.doi.org/10.1109/inis.2016.060.

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Menoyo, Sandra, Antonio Gentilella, and George Thomas. "Abstract B05: Characterization of the pre-ribosomal complex, which mediates the p53 Impaired Ribosome Biogenesis Checkpoint (IRBC)." 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-b05.

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Risi, Sebastian, Daniel Cellucci, and Hod Lipson. "Ribosomal robots." In Proceeding of the fifteenth annual conference. New York, New York, USA: ACM Press, 2013. http://dx.doi.org/10.1145/2463372.2463403.

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Wilson-Edell, Kathleen A., Gary K. Scott, Bianca S. Gabriel, Mariya Yevtushenko, Jason M. Held, Ingrid M. Hanson, and Christopher C. Benz. "Abstract 5179: Manipulating the ribosomal protein RPL24 by depletion, truncation, or acetylation alters ribosome formation and inhibits cancer cell growth." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-5179.

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Ivanova, SM, GG Karpova, NV Bogachiova, TA Riazantctva, and AI Speranskey. "THU0061 Ribosomal p protein antibodies." In Annual European Congress of Rheumatology, Annals of the rheumatic diseases ARD July 2001. BMJ Publishing Group Ltd and European League Against Rheumatism, 2001. http://dx.doi.org/10.1136/annrheumdis-2001.905.

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Chatterjee, Pratima, and Prasun Ghosal. "Introducing Parallelism in Ribosomal Computing." In NANOCOM '21: The Eighth Annual ACM International Conference on Nanoscale Computing and Communication. New York, NY, USA: ACM, 2021. http://dx.doi.org/10.1145/3477206.3477473.

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Yang, Yu, Dimitrios Stathis, Prashant Sharma, Kolin Paul, Ahmed Hemani, Manfred Grabherr, and Rafi Ahmad. "RiBoSOM." In SAMOS XVIII: Architectures, Modeling, and Simulation. New York, NY, USA: ACM, 2018. http://dx.doi.org/10.1145/3229631.3229650.

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Hannan, Ross, Jennifer Devlin, Katherine Hannan, Nadine Hein, Megan Bywater, Gretchen Poortinga, Don Cameron, et al. "Abstract PR16: Combined inhibition of ribosome function and ribosomal RNA gene transcription cooperate to delay relapse and extend survival in MYC-driven tumors." In Abstracts: Third AACR International Conference on Frontiers in Basic Cancer Research - September 18-22, 2013; National Harbor, MD. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.fbcr13-pr16.

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Reports on the topic "Ribosomas"

1

Hubbard, J. Computer modeling 16S ribosomal RNA. Office of Scientific and Technical Information (OSTI), April 1990. http://dx.doi.org/10.2172/6749631.

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García Ortega, Lucía. Saber cómo es un ribosoma merecía el premio Nobel. Sociedad Española de Bioquímica y Biología Molecular (SEBBM), February 2010. http://dx.doi.org/10.18567/sebbmdiv_rpc.2010.02.1.

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Llorca, Óscar. Biología estructural del ribosoma, una gran maquinaria para la síntesis de proteínas. Sociedad Española de Bioquímica y Biología Molecular (SEBBM), January 2010. http://dx.doi.org/10.18567/sebbmdiv_anc.2010.01.1.

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Kemp, P. F., S. Lee, and J. LaRoche. Evaluating bacterial activity from cell-specific ribosomal RNA content measured with oligonucleotide probes. Office of Scientific and Technical Information (OSTI), January 1992. http://dx.doi.org/10.2172/6973949.

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Kemp, P. F., S. Lee, and J. LaRoche. Evaluating bacterial activity from cell-specific ribosomal RNA content measured with oligonucleotide probes. Office of Scientific and Technical Information (OSTI), October 1992. http://dx.doi.org/10.2172/10181975.

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Taylor, Ronald C. Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology. Office of Scientific and Technical Information (OSTI), November 1991. http://dx.doi.org/10.2172/10108317.

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Taylor, R. C. Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology. Office of Scientific and Technical Information (OSTI), November 1991. http://dx.doi.org/10.2172/6057182.

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Woese, Carl R., Nigel Goldenfeld, and Zaida Luthey-Schulten. Role of horizontal gene transfer as a control on the coevolution of ribosomal proteins and the genetic code. Office of Scientific and Technical Information (OSTI), March 2011. http://dx.doi.org/10.2172/1010449.

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Pace, N. R. Phylogenetic analysis of hyperthermophilic natural populations using ribosomal RNA sequences. Final report, July 15, 1995--July 14, 1996. Office of Scientific and Technical Information (OSTI), June 1997. http://dx.doi.org/10.2172/491420.

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