1,720,972 research outputs found
A novel architectural role for Top2 in S phase
No full textThe maintenance of genome integrity is a process of main importance for cell survival. Cells experiencing DNA damage or replicative stresses show mutations accumulations and chromosomes aberrations that are known to be directly related to genetic disease and cancer formations.
DNA replication is a dangerous event by itself. Indeed genome integrity can be impaired by unscheduled recombination events, chromosome lesions, replication on a damage template, or replication stress induced by drugs affecting fork progression.
Moreover the separation of the two strands of DNA during replication and the progression of the replication bubble physiologically generate topological problems, as positive supercoiling (helical overwinding) or precatenates formation (interwines in the daughter duplexes). DNA topoisomerases are enzyme able to modify the topological state of DNA molecules mediating a transient breakage of one or both he helices of the molecule. The study of these enzymes is of large interest because most commonly used antitumoral drugs act stabilizing topoisomerase-cleaved DNA structure, mediating a citotoxic effect. During replication stress DNA topoisomerases II have been involved in replicon resetting at mitosis through remodeling of chromosomal loops. Other proteins involved in the chromatin architecture are part of the High Mobility Group. The HMG proteins have been implicated in almost every DNA metabolic process, as transcription regulation and maintenance of chromosomal integrity. Moreover, in human HMGB1 (protein related to the Hmo1 protein of yeast) physically interacts and stimulates TopoIIα.
We have previously show that during S phase Top2 localize to intergenic regions.
In this project using the budding yeast Saccharomyces cerevisiae as experimental model, we showed a genetic interaction between Top2 and Hmo1. Moreover we were able to mark different sites bind by Top2 and Hmo1 that became fragile in absence of Top2, and to characterize the fork progression at some of these sites, defining a novel architectural role for Top2 in S phase
Analysis of Top1 and Top2 contribution to chromosomal DNA replication
No full textProliferating cells must accurately duplicate their genomes and segregate them into daughter cells in order to
preserve their genetic information. Several events can compromise genome integrity during DNA replication,
such as dNTPs misincorporation or damaging of the template.
DNA replication can also be challenged by the accumulation of topological constraints generated by the
separation of the two strands of the DNA double helix. The stress created by the progressing replication
machinery can be converted into positive supercoiling (helical overwinding) or precatenates (intertwines the
daughter duplexes). Accumulation of supercoiling can cause a block to the progression of replication forks,
while accumulation of precatenates represents a physical linkage between chromosomes that impede their
correct segregation. DNA topoisomerases are enzymes able to modify the topological state of DNA molecules.
Type IB topoisomerases mediate the passage of one strand through another and can efficiently remove
supercoiling. Differently, type II topoisomerases mediate the passage of one duplex through another and can
act both on supercoiling and precatenates. Moreover, this class of enzymes can unlink sister chromatids prior
to chromosome segregation. It is currently unknown what is the cellular response to the accumulation of
unresolved topological constraints generated by the replication machinery during S-phase.
Cells have evolved different surveillance mechanisms to monitor the correct progression through the
different phases of the cell cycle, which are known as checkpoints.
In particular, during the S phase, two different checkpoint pathways act to preserve genome integrity: the
replication checkpoint and the intra-S phase DNA damage checkpoint.
When replication is inhibited or DNA lesions arise in S-phase, a signalling cascade is activated leading to the
block of the cell cycle progression and promoting the resolution of replication impediments or the repair of
the DNA damage. Rad53 is an essential kinase in this cascade, and is rapidly activated by phosphorylation in
response to DNA damage. For this reason the phosphorylation status of this protein can be used as an
indicator of checkpoint activation.
In this project we investigated the roles of Top1 (Type IB) and Top2 (Type IIA) DNA topoisomerases during
the synthesis (S) phase of the cell cycle, and their contribution to genomic DNA replication. By
contemporarily inactivating both topoisomerases in budding yeast Saccharomyces cerevisiae cells, we were
able to investigate how the accumulation of torsional stress affects replication fork stability and DNA damage
checkpoint response
THE DNA DAMAGE CHECKPOINT PRESERVES REPLICATION FORK INTEGRITY BY REGULATING TRANSCRIBED GENES ASSOCIATION TO THE NUCLEAR PORE COMPLEX.
No full textGenome instability, defined as the occurrence and amplification of mutations and chromosomal rearrangements, is a hallmark of neoplasic transformation and cancer onset. Cells have evolved DNA damage checkpoint processes that act in response to replicative stress induced by genotoxic agents. In Saccharomyces cerevisiae the DNA damage checkpoint requires the essential- Rad53 kinase. Checkpoint-defective cells accumulate gross chromosomal rearrangements and loose viability following exposure to hydroxyurea (HU), mainly due to their failure to stabilize stalled replication forks. In this work I show that mutations in THO/TREX and TREX2 genes, that encode factors required for mRNA transcription, export and association of transcribed genes to the nuclear envelope (Gene gating), rescue the viability of rad53 checkpoint deficient mutants treated with low concentrations of HU. This suppression is not affected by the RNAse H overexpression, suggesting that is not related to R-loop formation, transcription defects or hyper-recombination. By 2D gels and BrdU-ChIP analyses, I found that SAC3 (TREX2) deletion suppresses replication fork progression defects and collapse in rad53 cells treated with HU. Ablation of genes encoding Nuclear Pore Complex inner basket factors, that are required for gene gating, also suppresses the HU-sensitivity ofcheckpoint mutants. Moreover I found that upon replication stress, transcribed gene dissociate from the nuclear envelope in a Rad53-dependent manner. Based on these results, I propose that in cells experiencing replication stress the DNA damage checkpoint stabilizes replication forks by releasing the topological constraints imposed by NPC-associated genes
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
Dispelling 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
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
- …
