1,720,967 research outputs found
RecF, UvrD, RecX and RecN proteins suppress DNA degradation at DNA double-strand breaks in Escherichia coli
No full textAbstract
Double strand breaks (DSBs) in E. coli chromosome (such as those induced by gamma rays) are repaired by recombination repair, during which a certain amount of DNA gets degraded. We monitored DNA degradation in gamma-irradiated cells to assess processing of DSBs. DNA degradation in irradiated cells is regulated by RecA protein concentration and its affinity of ssDNA binding, as well as by exonucleases that trim 3'-terminated ss tails. Here we determined the effects of proteins that affect formation and stability of RecA nucleofilaments on DNA degradation and cell survival. RecF and UvrD suppressed DNA degradation through RecA protein function and SOS induction, while also improving gamma survival. RecF and UvrD function in one pathway. Acting along with RecF, RecX suppressed DNA degradation and stimulated gamma-survival, which also depends on RecA protein and SOS induction. Furthermore, we determined a role in DNA degradation of several proteins that participate in DSB repair. RecN was required for DNA repair and for degradation suppression, acting on the RecABCD pathway. Furthermore, we show that SSB protein overproduction did not affect DNA degradation. Inactivation of RecG and RuvABC, proteins that catalyze the postsynaptic phase of recombination repair of DSBs, also did not affect DNA degradation, suggesting that once formed, recombination intermediates are not subject to DNA degradation, and that the postsynaptic phase is an irreversible, single-round process, unlike the presynaptic phase, which is mostly repetitive
Role of Polyadenylation in mRNA Genome Integration via LINE-1 Retrotransposons: An Opinion on mRNA Vaccine Safety
No full textThe polyadenylated (polyA) tail of mRNA plays a crucial role in regulating mRNA stability and translation, and it may also contribute to genome integration through interactions with long interspersed nuclear element-1 (LINE-1, L1) retrotransposons. This interaction is particularly relevant for mRNA vaccines. Understanding how the polyA tail interacts with L1 proteins, especially open reading frame 2 protein (ORF2p), is critical for assessing these risks and developing strategies to enhance the safety of mRNA vaccines. We suggest conducting in vitro experiments to explore polyA tail modifications and their effects on L1 binding
The monomeric resins tegdma and hema regulate the transcriptional control of matrix metalloproteinases mmp-2 and mmp-9 in human pulp fibroblasts and mesenchymal stem cells
No full textResidual monomers, as triethylene-glycol-dimethacrylate (TEGDMA), 2-hydroxylethyl-methacrylate (HEMA), can be released from dental based-resin materials, as result of incomplete polymerization and induce cytotoxicity, genotoxicity and delay the cell cycle. It has been shown that dental monomers altered the Matrix Metalloproteinases (MMPs) activity. The MMPs are a family of proteolytic enzymes involved in extracellular matrix degradation. Our group, will study the role of these resins in the control of the molecular and physiological processes in human pulp fibroblasts and mesenchymal stem cells, such as transcription of MMP2 and MMP9 genes, apoptosis and cytotoxicity
Satellite DNA Modulates Gene Expression in the Beetle Tribolium castaneum after Heat Stress (PLoS Genet, (2015), 11(9))
No full text
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
Reverse transcription-quantitative PCR (RT-qPCR) without the need for removal of template DNA
No full textThe qualitative and/or quantitative analysis of transcripts by PCR amplification is widely used to detect and quantify many different types of transcripts such as messenger RNA, ribosomal RNA, non-coding RNA etc. The most common applications include gene expression analysis and precise identification of a particular microorganism.
For the purified RNA to be quantified, it is subjected to reverse transcription (RT), by which the RNA molecules are converted into cDNA (complementary DNA) by the reverse transcriptase enzyme. The main problem of most currently used protocols lies in the often-present DNA contamination, which is impossible to chemically differentiate from the cDNA by the polymerase enzyme during PCR amplification, thus causing false positive results. To overcome this limitation, all current protocols include a couple of DNA elimination steps, both during the purification of RNA as well as in subsequent RT step. The DNA is eliminated either with the aid of specific mechanical filters (silica-based columns) or through enzymatic digestion by a specific enzyme, such as DNaseI (Deoxyribonuclease I). However, these treatments are not 100% effective, often leaving DNA contamination. Furthermore, any procedure implemented to reduce the concentration of DNA in the sample certainly causes the reduction of the RNA concentration as well, which is unstable and easily degradable molecule.
Here we report a novel method for transcriptome analysis by PCR, wherein cDNA and template DNA are differentiated and thus contamination by the latter is excluded, hence producing more precise, reliable and reproducible results
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