Translation selectively destroys non-functional transcription complexes

Transcription elongation stalls at lesions in the DNA template(1). For the DNA lesion to be repaired, the stalled transcription elongation complex (EC) has to be removed from the damaged site(2). Here we show that translation, which is coupled to transcription in bacteria, actively dislodges stalled ECs from the damaged DNA template. By contrast, paused, but otherwise elongation-competent, ECs are not dislodged by the ribosome. Instead, they are helped back into processive elongation. We also show that the ribosome slows down when approaching paused, but not stalled, ECs. Our results indicate that coupled ribosomes functionally and kinetically discriminate between paused ECs and stalled ECs, ensuring the selective destruction of only the latter. This functional discrimination is controlled by the RNA polymerase\u27s catalytic domain, the Trigger Loop. We show that the transcription-coupled DNA repair helicase UvrD, proposed to cause backtracking of stalled ECs(3), does not interfere with ribosome-mediated dislodging. By contrast, the transcription-coupled DNA repair translocase Mfd(4) acts synergistically with translation, and dislodges stalled ECs that were not destroyed by the ribosome. We also show that a coupled ribosome efficiently destroys misincorporated ECs that can cause conflicts with replication(5). We propose that coupling to translation is an ancient and one of the main mechanisms of clearing non-functional ECs from the genome

Experimental observation of the Aubry transition in two-dimensional colloidal monolayers

The possibility to achieve entirely frictionless, i.e. superlubric, sliding between solids, holds enormous potential for the operation of mechanical devices. At small length scales, where mechanical contacts are well-defined, Aubry predicted a transition from a superlubric to a pinned state when the mechanical load is increased. Evidence for this intriguing Aubry transition (AT), which should occur in one dimension (1D) and at zero temperature, was recently obtained in few-atom chains. Here, we experimentally and theoretically demonstrate the occurrence of the AT in an extended two-dimensional (2D) system at room temperature using a colloidal monolayer on an optical lattice. Unlike the continuous nature of the AT in 1D, we observe a first-order transition in 2D leading to a coexistence regime of pinned and unpinned areas. Our data demonstrate that the original concept of Aubry does not only survive in 2D but is relevant for the design of nanoscopic machines and devices at ambient temperature.Comment: 12 pages including 4 figures + 9 pages supplemental informatio

Is increased time to diagnosis and treatment in symptomatic cancer associated with poorer outcomes?:Systematic review

background: It is unclear whether more timely cancer diagnosis brings favourable outcomes, with much of the previous evidence, in some cancers, being equivocal. We set out to determine whether there is an association between time to diagnosis, treatment and clinical outcomes, across all cancers for symptomatic presentations. methods: Systematic review of the literature and narrative synthesis. results: We included 177 articles reporting 209 studies. These studies varied in study design, the time intervals assessed and the outcomes reported. Study quality was variable, with a small number of higher-quality studies. Heterogeneity precluded definitive findings. The cancers with more reports of an association between shorter times to diagnosis and more favourable outcomes were breast, colorectal, head and neck, testicular and melanoma. conclusions: This is the first review encompassing many cancer types, and we have demonstrated those cancers in which more evidence of an association between shorter times to diagnosis and more favourable outcomes exists, and where it is lacking. We believe that it is reasonable to assume that efforts to expedite the diagnosis of symptomatic cancer are likely to have benefits for patients in terms of improved survival, earlier-stage diagnosis and improved quality of life, although these benefits vary between cancers

State Of the Art Report in the fields of numerical analysis and scientific computing. Final version as of 16/02/2020 deliverable D4.1 of the HORIZON 2020 project EURAD.: European Joint Programme on Radioactive Waste Management

Document information Project Acronym EURAD Project Title European Joint Programme on Radioactive Waste Management Project Type European Joint Programme (EJP) EC grant agreement No. 847593 Project starting / end date 1 st June 2019-30 May 2024 Work Package No. 4 Work Package Title Development and Improvement Of NUmerical methods and Tools for modelling coupled processes Work Package Acronym DONUT Deliverable No. 4.

Evaluating the influence of a g-quadruplex prone sequence on the transactivation potential by wild-type and/or mutant p53 family proteins through a yeast-based functional assay

P53, P63, and P73 proteins belong to the P53 family of transcription factors, sharing a common gene organization that, from the P1 and P2 promoters, produces two groups of mRNAs encoding proteins with different N-terminal regions; moreover, alternative splicing events at Cterminus further contribute to the generation of multiple isoforms. P53 family proteins can influence a plethora of cellular pathways mainly through the direct binding to specific DNA sequences known as response elements (REs), and the transactivation of the corresponding target genes. However, the transcriptional activation by P53 family members can be regulated at multiple levels, including the DNA topology at responsive promoters. Here, by using a yeast-based functional assay, we evaluated the influence that a G-quadruplex (G4) prone sequence adjacent to the p53 RE derived from the apoptotic PUMA target gene can exert on the transactivation potential of full-length and Nterminal truncated P53 family \u3b1 isoforms (wild-type and mutant). Our results show that the presence of a G4 prone sequence upstream or downstream of the P53 RE leads to significant changes in the relative activity of P53 family proteins, emphasizing the potential role of structural DNA features as modifiers of P53 family functions at target promoter sites