1,721,025 research outputs found
Global alterations in mRNA polysomal recruitment in a cell model of colorectal cancer progression to metastasis
No full textTumour onset and progression are due to the accumulation
of genomic lesions, which alter gene expression and ultimately
proteome activities. These lesions are thought to
affect primarily the transcriptional control of gene
expression. In the present study, we aimed at evaluating
the genome-wide occurrence of alterations in the translational
control exploiting an isogenic, phenotypically
validated cellular model of colorectal cancer (CRC) transition
from invasive carcinoma to metastasis. In this
model, microarray profiling shows that changes in the
level of messenger ribonucleic acid (mRNA) association
with polysomes occur more than 2-fold than changes in
the level of total cellular mRNA. When common to both
the total and polysomal compartments, these changes are
also homodirectional, being amplified in magnitude at the
polysomal level. Comparison between the transcriptional
and the translational fluctuations revealed distinct signatures
of statistically over-represented gene functions,
involving the program of cell proliferation for both
levels of analysis, while the apoptosis and the translation
programs were affected mainly at translation. Looking
for an upstream determinant of translational deregulation,
we found an increase in the hyperphosphorylated
form of the 4E-BP1 protein in the metastatic cell
line, possibly resulting in an increased activation of
cap-dependent translation due to increased activity of
the eIF4E protein. Analysis of the distribution profiles
for the 50 untranslated region (50-UTR) length of the
changed genes showed an association between longer 50-UTRs and the probability for the relevant gene to
be altered translationally, consistent with enhanced
eIF4E function. This genome-wide analysis is in favour
of a model of profound alteration of translational
control in late CRC progression. It also suggests polysomal
mRNA profiles as a new, informative dimension for
the study of transcriptome imbalance in cancer
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Role of PIM1 in the activation of p53 induced by RPS19 deficiency in colon and prostate cancer cell lines
No full textDispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Molecular mechanisms activated in response to ribosomal stress
No full textThe ribosome biogenesis is an energetic expensive process that is finely regulated according to the growth conditions and to the cellular stress. Any defect in this process induces in the cell a ribosomal stress, generally leading to the inhibition of cell proliferation and the activation of apoptosis mostly through a p53-dependent mechanism (Fumagalli et al., 2009; Pestov et al., 2001). Some genetic diseases, such as Diamond Blackfan Anemia, have been shown to be associated to defective ribosome biogenesis and therefore have been named ribosomopathies. To study the molecular mechanisms activated in response to ribosomal stress, we altered the production of one or more ribosomal proteins in different cell lines by siRNA-mediated down regulation. In the first part of the project we analyzed the signaling pathways activated in response to ribosomal stress. In particular we selected cellular components known to be involved in ribosome synthesis: 1) mTORC1 2) mTORC2 and 3) AMPK. Analysis of RPS19-depleted prostate cancer cell line PC3 showed that the phosphorylation status of mTORC1 downstream targets S6 kinase 1 (S6K1) and 4E-BP1 was not altered after ribosomal stress. Then we analyzed the serine/threonine kinase AKT, because of its role in the mTORC2-ribosome pathway (Zinzalla et al., 2011). Western blot analysis revealed that the AKT phosphorylation was decreased after depletion of RPS19 in three different prostate cancer cell lines: 22RV1, DU145 and PC3. The same phenomenon was observed in PC3 cells after depletion of other ribosomal proteins (RPS6 and RPS7). Therefore, consistent with Zinzalla et al., we can conclude that mTORC2 is probably involved in the response to ribosomal stress. The last pathway that we analyzed was the AMP-kinase (AMPK), a kinase activated under conditions of metabolic stress. The depletion of different ribosomal proteins (RPS19, RPS6 and RPS7) showed that there was an increase in the phosphorylation level of AMPK indicating its activation in the different prostate cancer cell lines analyzed. This result was consistent with Danilova and colleagues that observed an activation of AMPK in ribosomal protein-depleted zebrafish model (Danilova et al., 2014). In addition, we addressed the phosphorylation status of eukaryotic elongation factor 2 (eEF2) as a downstream target of AMPK. We found that in 22RV1, DU145 and PC3 cells depletion of RPS6, RPS19, RPS7 induced an increase of eEF2 phosphorylation. This could explain the translation elongation inhibition recently reported by our group (Gismondi et al., 2014). In the second part of the project we analyzed the effect of the depletion of RPS19 or other ribosomal proteins on rRNA synthesis. Consistent with a number of publications (Badhai et al., 2009; Choesmel et al., 2007), we observed an alteration of rRNA maturation at the level of 21S precursor. In addition, we observed that RPS19 depletion caused a reduction of the 47S rRNA level in K562C, 22RV1 and HEK293 cells. The same effect was observed after depletion of RPS6 and RPL11. Since the analysis of 47S rRNA stability did not show any alteration (unpublished data), we addressed RNA Polymerase I (Pol I) activity. For this purpose we performed ChIP assay in HEK293 cells after depletion of RPS19. We found that ribosomal stress caused a decrease of Pol I recruitment on two different portions of ribosomal DNA (rDNA). Moreover we observed alteration of the binding of Pol I transcription factor UBF. Therefore, these results indicated that ribosomal stress altered not only Pol I recruitment but also the assembly/activity of Pol I complex. Finally, in order to investigate the signaling pathway responsible for the decrease of Pol I activity, we analyzed AKT and AMPK, both known to be involved in the regulation of Pol I (Chan et al., 2011). The overexpression of a constitutively active form of AKT in HEK293 cells shown that this kinase was not involved in the decrease of rRNA synthesis during ribosomal stress. Similarly, inhibition of AMPK by RNA interference or Compound C in 22RV1 cells revealed that the downregulation of this kinase was not sufficient to rescue rRNA synthesis after ribosomal stress. Therefore, the signaling pathways that could mediate the downregulation of rRNA synthesis after ribosomal stress remains to be addressed
Ribosomal stress regulates eEF2K activity and expression
No full textTranslation is a complex process essential for cell survival that is subjected to a strict regulation. Although it is commonly considered a general phenomenon, it can be divided into two aspects: 1) general protein synthesis and 2) translation of specific messengers. During the course of my PhD work I had the opportunity to study both these aspects, focusing my attention on translation elongation during ribosomal stress and the translational regulation of specific mRNAs as a form of post transcriptional regulation. This thesis work is focused mainly on the principal project which identified a novel interaction important for ribosomal stress response and regulation of the elongation step. In addition, I have taken part to several different side projects some of which performed in collaboration with other research groups. Some of those works have been published in scientific journals, collected and briefly explained in the Appendix. Within those I have focused my attention on the translational analysis of specific mRNAs. In particular, I have investigated how they can be differently translated in response to the induction of specific stimuli or by regulatory proteins activity
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