Estudio topológico del ADN nucleosomal y su paradoja del número de enlace

[spa] El empaquetamiento del ADN en fibras de cromatina implica una gran cantidad de deformaciones geométricas de la doble hélice (enrollamiento y superenrollamiento del ADN) y la formación de una jerarquía de asas o dominios de distinto tamaño. Este empaquetamiento conlleva severas restricciones topológicas, las cuales juegan un papel determinante en los procesos metabólicos del ADN. Sin embargo, la arquitectura fina de la cromatina en 3D/4D, así como la trayectoria espacial y la topología de las cadenas de ADN a través de cada elemento individual de la cromatina, permanecen como aspectos enigmáticos y poco explorados. Ello es debido tanto a limitaciones metodológicas como a su dificultad conceptual, que hacen de la topología del ADN un área de estudio casi desconocida para gran parte de la comunidad científica. En los años 80, diversos estudios experimentales establecieron que la unidad estructural de la cromatina, el nucleosoma, estabilizaba una diferencia del número de enlace (∆Lk) igual a -1.0/por nucleosoma. Este valor, sin embargo, suponía una incongruencia respecto al valor teórico estimado a partir de otros estudios estructurales de los nucleosomas, que concluían que el valor ∆Lk debería ser > -1.0 y cercano a -2. Esta incongruencia generó la llamada “Paradoja del número de enlace del ADN nucleosomal”, que ha estado vigente hasta la actualidad. En esta tesis se ha realizado un minucioso análisis de la topología del ADN nucleosomal para determinar con precisión el valor ∆Lk. Los resultados presentados demuestran que los nucleosomas estabilizan un valor medio de ∆Lk = -1.26. Este valor, junto a las correcciones de los valores teóricos derivados de los estudios estructurales previos, soluciona la paradoja del número de enlace del ADN nucleosomal. La aproximación metodológica, utilizando pequeños minicromosomas circulares para el análisis topológico de elementos de la cromatina in vivo, hace del presente trabajo una apuesta novedosa y original en el campo de la topología.[eng] Packaging of DNA molecules into chromatin imposes severe geometrical deformations and topological constraints in the double helix (DNA wrapping, looping and supercoiling). These restrictions play an important role in the regulation of genome activities. Whereas the 3D/4D architecture of chromatin is being uncovered down to Kb resolution, the local path and the topology of the DNA strands constrained by individual chromatin elements remains elusive due to methodological limitations and conceptual complexity. In the ‘80s, it was established that the structural unit of chromatin, the nucleosome, constrains on average about one negative DNA supercoil (i.e. a DNA linking number difference, ∆Lk, of -1/ per nucleosome). However, this ∆Lk value was inconsistent with the theoretical value estimated from structural studies (∆Lk ≈ -2). This incongruence between the theoretical and the experimental value produced the so-called “linking number paradox”. In this thesis, we developed an approach to analyze the topology of DNA constrained by individual chromatin elements in vivo, so we could accurately determine the ∆Lk value stabilized by individual nucleosomes. Our result indicates that nucleosomes stabilize an average value of ∆Lk = -1.26. This value balances the twist (∆Tw ≈ +0.2) and writhe (∆Wr ≈ -1.5) deformations of nucleosomal DNA in terms of the equation ∆Lk = ∆Tw + ∆Wr. Our finding could solve the long standing “linking number paradox” of nucleosomal DNA

Education and Political Participation of Women: The Case of Portugal

This research aims to analyses the women’s participation in Portugal politics in consequence of its educational attainment. On the one hand, the Constitution of the Portuguese Republic of April 2, 1976, gives women (and men) a right to equal opportunities for school success, to access to the higher education and to better working conditions. On the other hand, the same Constitution defends, in article 9, that fundamental task of the State is to promote equality between men and women and, in article 109, refers the citizens’ rights to political participation. However, despite the expansion of the education system, showing the rapid progress in improving baseline qualifications, women's educational attainment in certain working areas remains a challenge. Thus, methodologically, this research relied on a two-track approach. The first approach takes the form of a literature review, based, primarily in the legal regime of Portuguese higher education system and, in addition, on the gender parity law, considering that, according to Decree-Law nº 402/73 of August 11, Portugal promoted the democratization of education that was consolidated in the expansion and diversification of higher education to match the need to ensure economic development of the country. The second approach takes the form of an empirical research based on a descriptive statistical analysis, supported on the statistical information provided by Portuguese Ministry of Education and Science that show the increases of the Portuguese’ qualifications as well as the Portuguese Assembly of the Republic that provides important insights on the adoption of gender quotas in Portugal. In this sense, the research provides empirical evidence about the role of women’s education in advancing their interests at the Government and politics

DNA Topology and Global Architecture of Point Centromeres

SummaryDNA is wrapped in a left-handed fashion around histone octasomes containing the centromeric histone H3 variant CENP-A. However, DNA topology studies have suggested that DNA is wrapped in a right-handed manner around the CENP-A nucleosome that occupies the yeast point centromere. Here, we determine the DNA linking number difference (ΔLk) stabilized by the yeast centromere and the contribution of the centromere determining elements (CDEI, CDEII, and CDEIII). We show that the intrinsic architecture of the yeast centromere stabilizes +0.6 units of ΔLk. This topology depends on the integrity of CDEII and CDEIII, but it is independent of cbf1 binding to CDEI and of the variable length of CDEII. These findings suggest that the interaction of the CBF3 complex with CDEIII and a distal CDEII segment configures a right-handed DNA loop that excludes CDEI. This loop is then occupied by a CENP-A histone complex, which does not have to be inherently right-handed

The effect of the Covid-19 epidemic on the self-perception of training needs in STEAM lecturers

This work in progress research-to-practice paper presents the initial results of a study carried out at our university among lecturers, aimed at determining how the perception of training needs have changed due to the pandemic, and if this change can be used to increase enrollment in the university training program. Pedagogical training of university lecturers has usually been a self-training process guided by their own beliefs about what good teaching is, and the self-perception of one’s own strengths and weaknesses with respect to teaching. The COVID-19 pandemic shook the world in many ways, but it also challenged lecturers about their own convictions regarding educational methodologies, evaluation and their own approach to teaching, so it is a great opportunity for change.Peer ReviewedObjectius de Desenvolupament Sostenible::4 - Educació de QualitatPostprint (author's final draft

La Conceptualització del Metacampus d'Unite!

Aquesta publicació s’ha realitzat en el marc del projecte: / Esta publicación se ha realizado en el marco del proyecto: / This publication has been made with the framework of the project: ACEDIM: Avaluació i certificació de la competència digital docent en la formació inicial de mestres: una proposta de model per al sistema universitari català. (ref. 2017ARMIF00031).L’Aliança Unite!, formada per set universitats tecnològiques europees, és una xarxa que estableix un nou model per a un campus interuniversitari europeu virtual i físic, de col·laboració estreta, mitjançant mobilitat física i virtual dels seus membres, programes conjunts, comunitats promotores d’innovació docent i xarxes d’innovació oberta i emprenedoria. Una peça clau d’aquest entramat és la plataforma de campus virtual Metacampus. Convivint amb els campus virtuals de les altres universitats, el Metacampus té com a funció ser un punt de trobada comuna de tot membre de l’ecosistema Unite! amb reptes importants, com ara esdevenir una eina útil i usable per un conjunt heterogeni d’usuaris, acostumats a formes i processos força diferents. S’ha optat per utilitzar com a base la plataforma Moodle i maximitzar l’ús de les seves funcionalitats, mentre que es redueix al màxim el nombre de nous desenvolupaments que ajudin a aconseguir els objectius establerts. Després de tres mesos en la fase beta, el número d’usuaris registrats i participants en les activitats proposades fins ara permeten concloure que el camí iniciat ara fa mig any és l’adequat per abordar un repte com ara el disseny i la implantació d’un campus virtual multi universitari.Objectius de Desenvolupament Sostenible::4 - Educació de QualitatObjectius de Desenvolupament Sostenible::4 - Educació de Qualitat::4.3 - Per a 2030, assegurar l’accés en condicions d’igualtat per a tots els homes i dones a una formació tècnica, professional i superior de qualitat, inclòs l’ensenyament universitariObjectius de Desenvolupament Sostenible::4 - Educació de Qualitat::4.4 - Per a 2030, augmentar substancialment el nombre de joves i persones adultes que tenen les competències necessàries, en particular tècniques i professionals, per a accedir a l’ocupació, el treball digne i l’emprenedoriaObjectius de Desenvolupament Sostenible::4 - Educació de Qualitat::4.5 - Per a 2030, eliminar les disparitats de gènere en l’educació i garantir l’accés en condicions d’igualtat a les persones vulnerables, incloses les persones amb discapacitat, els pobles indígenes i els nens i nenes en situacions de vulnerabilitat, a tots els nivells de l’ensenyament i la formació professionalObjectius de Desenvolupament Sostenible::4 - Educació de Qualitat::4.7 - Per a 2030, garantir que tot l’alumnat adquireixi els coneixements teòrics i pràctics necessaris per a pro­moure el desenvolupament sostenible, a través, entre d’altres, de l’educació per al desenvolupament sostenible i l’adopció d’estils de vida sostenibles, els drets humans, la igualtat de gènere, la promoció d’una cultura de pau i no-violència, la ciutadania mundial i la valoració de la diversitat cultural i de la contribució de la cultura al desenvolupament sosteniblePostprint (published version

Human-AI Co-Creation Approach to Find Forever Chemicals Replacements

Generative models are a powerful tool in AI for material discovery. We are designing a software framework that supports a human-AI co-creation process to accelerate finding replacements for the ``forever chemicals''-- chemicals that enable our modern lives, but are harmful to the environment and the human health. Our approach combines AI capabilities with the domain-specific tacit knowledge of subject matter experts to accelerate the material discovery. Our co-creation process starts with the interaction between the subject matter experts and a generative model that can generate new molecule designs. In this position paper, we discuss our hypothesis that these subject matter experts can benefit from a more iterative interaction with the generative model, asking for smaller samples and ``guiding'' the exploration of the discovery space with their knowledge.Comment: 5 pages, Generative AI and HCI (GenAICHI) Workshop at CHI 23 (ACM CHI Conference on Human Factors in Computing Systems

Uridine 5′-triphosphate promotes in vitro Schwannoma cell migration through matrix metalloproteinase-2 activation

In response to peripheral nerve injury, Schwann cells adopt a migratory phenotype and modify the extracellular matrix to make it permissive for cell migration and axonal re-growth. Uridine 5′-triphosphate (UTP) and other nucleotides are released during nerve injury and activate purinergic receptors expressed on the Schwann cell surface, but little is known about the involvement of purine signalling in wound healing. We studied the effect of UTP on Schwannoma cell migration and wound closure and the intracellular signaling pathways involved. We found that UTP treatment induced Schwannoma cell migration through activation of P2Y2 receptors and through the increase of extracellular matrix metalloproteinase-2 (MMP-2) activation and expression. Knockdown P2Y2 receptor or MMP-2 expression greatly reduced wound closure and MMP-2 activation induced by UTP. MMP-2 activation evoked by injury or UTP was also mediated by phosphorylation of all 3 major mitogen-activated protein kinases (MAPKs): JNK, ERK1/2, and p38. Inhibition of these MAPK pathways decreased both MMP-2 activation and cell migration. Interestingly, MAPK phosphorylation evoked by UTP exhibited a biphasic pattern, with an early transient phosphorylation 5 min after treatment, and a late and sustained phosphorylation that appeared at 6 h and lasted up to 24 h. Inhibition of MMP-2 activity selectively blocked the late, but not the transient, phase of MAPK activation. These results suggest that MMP-2 activation and late MAPK phosphorylation are part of a positive feedback mechanism to maintain the migratory phenotype for wound healing. In conclusion, our findings show that treatment with UTP stimulates in vitro Schwannoma cell migration and wound repair through a MMP-2-dependent mechanism via P2Y2 receptors and MAPK pathway activation. © 2014 Lamarca et al.This research was supported by an unrestricted research grant from Ferrer S.A. (Barcelona, Spain) and by grant SAF2011-23550 from Ministerio de Economia y Competitividad of SpainPeer Reviewe

Silibinin suppresses EMT-driven erlotinib resistance by reversing the high miR-21/low miR-200c signature in vivo

The flavolignan silibinin was studied for its ability to restore drug sensitivity to EGFR-mutant NSCLC xenografts with epithelial-to-mesenchymal transition (EMT)-driven resistance to erlotinib. As a single agent, silibinin significantly decreased the tumor volumes of erlotinib-refractory NSCLC xenografts by approximately 50%. Furthermore, the complete abrogation of tumor growth was observed with the co-treatment of erlotinib and silibinin. Silibinin fully reversed the EMT-related high miR-21/low miR-200c microRNA signature and repressed the mesenchymal markers SNAIL, ZEB, and N-cadherin observed in erlotinib-refractory tumors. Silibinin was sufficient to fully activate a reciprocal mesenchymal-to-epithelial transition (MET) in erlotinib-refractory cells and prevent the highly migratogenic phenotype of erlotinib-resistant NSCLC cells. Given that the various mechanisms of resistance to erlotinib result from EMT, regardless of the EGFR mutation status, a water-soluble, silibinin-rich milk thistle extract might be a suitable candidate therapy for upcoming clinical trials aimed at preventing or reversing NSCLC progression following erlotinib treatment

Evolution of recombination in eutherian mammals: insights into mechanisms that affect recombination rates and crossover interference

Recombination allows faithful chromosomal segregation during meiosis and contributes to the production of new heritable allelic variants that are essential for the maintenance of genetic diversity. Therefore, an appreciation of how this variation is created and maintained is of critical importance to our understanding of biodiversity and evolutionary change. Here, we analysed the recombination features from species representing the major eutherian taxonomic groups Afrotheria, Rodentia, Primates and Carnivora to better understand the dynamics of mammalian recombination. Our results suggest a phylogenetic component in recombination rates (RRs), which appears to be directional, strongly punctuated and subject to selection. Species that diversified earlier in the evolutionary tree have lower RRs than those from more derived phylogenetic branches. Furthermore, chromosome-specific recombination maps in distantly related taxa show that crossover interference is especially weak in the species with highest RRs detected thus far, the tiger. This is the first example of a mammalian species exhibiting such low levels of crossover interference, highlighting the uniqueness of this species and its relevance for the study of the mechanisms controlling crossover formation, distribution and resolution.A.R-H.'s laboratory is funded by Ministerio de Ciencia e Innovacion (MICINN-Spain, CGL2010 20170) and the Barcelona Zoological Gardens (BSM, Zoo Barcelona). T.J.R.'s research is supported by a grant from the South African National Research Foundation. M.O.-B. is funded by Instituto de Salud Carlos III (CP07/0258 and PI08/1185).Peer reviewe

Transcriptional supercoiling boosts topoisomerase II-mediated knotting of intracellular DNA

Recent studies have revealed that the DNA cross-inversion mechanism of topoisomerase II (topo II) not only removes DNA supercoils and DNA replication intertwines, but also produces small amounts of DNA knots within the clusters of nucleosomes that conform to eukaryotic chromatin. Here, we examine how transcriptional supercoiling of intracellular DNA affects the occurrence of these knots. We show that although (-) supercoiling does not change the basal DNA knotting probability, (+) supercoiling of DNA generated in front of the transcribing complexes increases DNA knot formation over 25-fold. The increase of topo II-mediated DNA knotting occurs both upon accumulation of (+) supercoiling in topoisomerase-deficient cells and during normal transcriptional supercoiling of DNA in TOP1 TOP2 cells. We also show that the high knotting probability (Pkn 65 0.5) of (+) supercoiled DNA reflects a 5-fold volume compaction of the nucleosomal fibers in vivo. Our findings indicate that topo II-mediated DNA knotting could be inherent to transcriptional supercoiling of DNA and other chromatin condensation processes and establish, therefore, a new crucial role of topoisomerase II in resetting the knotting-unknotting homeostasis of DNA during chromatin dynamics