37 research outputs found
Function of the Pseudomonas aeruginosa NrdR Transcription Factor: Global Transcriptomic Analysis and Its Role on Ribonucleotide Reductase Gene Expression
Ribonucleotide reductases (RNRs) are a family of sophisticated enzymes responsible for the synthesis of the deoxyribonucleotides (dNTPs), the building blocks for DNA synthesis and repair. Although any living cell must contain one RNR activity to continue living, bacteria have the capacity to encode different RNR classes in the same genome, allowing them to adapt to different environments and growing conditions. Pseudomonas aeruginosa is well known for its adaptability and surprisingly encodes all three known RNR classes (Ia, II and III). There must be a complex transcriptional regulation network behind this RNR activity, dictating which RNR class will be expressed according to specific growing conditions. In this work, we aim to uncover the role of the transcriptional regulator NrdR in P. aeruginosa. We demonstrate that NrdR regulates all three RNR classes, being involved in differential control depending on whether the growth conditions are aerobic or anaerobic. Moreover, we also identify for the first time that NrdR is not only involved in controlling RNR expression but also regulates topoisomerase I (topA) transcription. Finally, to obtain the entire picture of NrdR regulon, we performed a global transcriptomic analysis comparing the transcription profile of wild-type and nrdR mutant strains. The results provide many new data about the regulatory network that controls P. aeruginosa RNR transcription, bringing us a step closer to the understanding of this complex system
Regulation of ribonucleotide synthesis by the Pseudomonas aeruginosa two-component system AlgR in response to oxidative stress
Ribonucleotide reductases (RNR) catalyze the last step of deoxyribonucleotide synthesis, and are therefore essential to DNA-based life. Three forms of RNR exist: classes I, II, and III. While eukaryotic cells use only class Ia RNR, bacteria can harbor any combination of classes, granting them adaptability. The opportunistic pathogen Pseudomonas aeruginosa surprisingly encodes all three classes, allowing it to thrive in diferent environments. Here we study an aspect of the complex RNR regulation whose molecular mechanism has never been elucidated, the well-described induction through oxidative stress, and link it to the AlgZR two-component system, the primary regulator of the mucoid phenotype. Through bioinformatics, we identify AlgR binding locations in RNR promoters, which we characterize functionally through EMSA and physically through AFM imaging. Gene reporter assays in diferent growth models are used to study the AlgZR-mediated control on the RNR network under various environmental conditions and physiological states. Thereby, we show that the two-component system AlgZR, which is crucial for bacterial conversion to the mucoid phenotype associated with chronic disease, controls the RNR network and directs how the DNA synthesis pathway is modulated in mucoid and non-mucoid bioflms, allowing it to respond to oxidative stress
Electronic tongues to assess wine sensory descriptors
Altres ajuts: ICREA AcademiaThis work reports the application of an electronic tongue as a tool towards the analysis of wine in tasks such as its discrimination based on the maturing in barrels or the prediction of the global scores assigned by a sensory panel. To this aim, red wine samples were first analysed with the voltammetric sensor array, without performing any sample pretreatment. Afterwards, obtained responses were preprocessed employing fast Fourier transform (FFT) for the compression and reduction of signal complexity, and obtained coefficients were then used as inputs to build the qualitative and quantitative models employing either linear discriminant analysis (LDA) or partial least squares regression (PLS), respectively. Satisfactory results were obtained overall, with a classification rate of 100% in the discrimination of the type of barrel used during wine maturing, a normalized NRMSE of 0.077 in the estimation of ageing time (months) or 0.11 in the prediction of the scores (0-10) from a trained sensory panel (all for the external test subset)
Expression analysis of candidate genes for fatty acid composition in adipose tissue and identifcation of regulatory regions
The aim of this work was to study the genetic basis of the backfat expression of lipid-related genes
associated with meat quality traits in pigs. We performed a genome-wide association study with the
backfat gene expression measured in 44 genes by qPCR and the PorcineSNP60 BeadChip genotypes
in 115 Iberian x Landrace backcross animals. A total of 193 expression-associated SNPs located in 19
chromosomal regions were associated with expression levels of ACSM5, ELOVL6, FABP4, FADS2, and
SLC27A4 genes. Three expression quantitative trail loci (eQTLs) corresponding to ACSM5, FABP4, and
FADS2 were classifed as cis-acting eQTLs, whereas the remaining 16 eQTLs have trans-regulatory
efects. Remarkably, a SNP in the ACSM5 promoter region and a SNP in the 3′UTR region of FABP4
were the most associated polymorphisms with the ACSM5 and FABP4 expression levels, respectively.
Moreover, relevant lipid-related genes mapped in the trans-eQTLs regions associated with the ACSM5,
FABP4, FADS2, and SLC27A4 genes. Interestingly, a trans-eQTL hotspot on SSC13 regulating the gene
expression of ELOVL6, ELOLV5, and SCD, three important genes implicated in the elongation and
desaturation of fatty acids, was identifed. These fndings provide new data to further understand the
functional regulatory mechanisms implicated in the variation of fatty acid composition in pigs.info:eu-repo/semantics/publishedVersio
Expression analysis of candidate genes for fatty acid composition in adipose tissue and identification of regulatory regions
Altres ajuts: PhD grant from the Universitat Autònoma de Barcelona (458-01-1/2011)The aim of this work was to study the genetic basis of the backfat expression of lipid-related genes associated with meat quality traits in pigs. We performed a genome-wide association study with the backfat gene expression measured in 44 genes by qPCR and the PorcineSNP60 BeadChip genotypes in 115 Iberian x Landrace backcross animals. A total of 193 expression-associated SNPs located in 19 chromosomal regions were associated with expression levels of ACSM5, ELOVL6, FABP4, FADS2, and SLC27A4 genes. Three expression quantitative trail loci (eQTLs) corresponding to ACSM5, FABP4, and FADS2 were classified as cis-acting eQTLs, whereas the remaining 16 eQTLs have trans-regulatory effects. Remarkably, a SNP in the ACSM5 promoter region and a SNP in the 3'UTR region of FABP4 were the most associated polymorphisms with the ACSM5 and FABP4 expression levels, respectively. Moreover, relevant lipid-related genes mapped in the trans-eQTLs regions associated with the ACSM5, FABP4, FADS2, and SLC27A4 genes. Interestingly, a trans-eQTL hotspot on SSC13 regulating the gene expression of ELOVL6, ELOLV5, and SCD, three important genes implicated in the elongation and desaturation of fatty acids, was identified. These findings provide new data to further understand the functional regulatory mechanisms implicated in the variation of fatty acid composition in pigs
Social inequities in the impact of COVID-19 lockdown measures on the mental health of a large sample of the Colombian population (PSY-COVID study)
The identification of general population groups particularly vulnerable to the impact of COVID-19 lockdown measures on mental health and the development of healthcare policies are priority challenges in the current and future pandemics. This study aimed to identify the personal and social determinants of the impact of COVID-19 lockdown measures on mental health in a large sample of the Colombian population. In this cross-sectional study, an anonymous online survey was answered by 18,061 participants from the general population residing in Colombia during the first wave of the COVID-19 outbreak (from 20 May to 20 June 2020). The risk of depression, anxiety, and somatization disorders were measured using the Patient Health Questionnaire (PHQ-2), Generalized Anxiety Disorder Scale (GAD-2), and Somatic Symptom Questionnaire (SSQ-5), respectively. Overall, 35% of participants showed risk of depression, 29% of anxiety, and 31% of somatization. According to the analysis of social determinants of health, the most affected groups were people with low incomes, students, and young adults (18-29 years). Specifically, low-income young females were the most at-risk population group. These findings show how the lockdown measures affected the general population's mental health in Colombia and highlight some social risk factors in health
CIBERER : Spanish national network for research on rare diseases: A highly productive collaborative initiative
Altres ajuts: Instituto de Salud Carlos III (ISCIII); Ministerio de Ciencia e Innovación.CIBER (Center for Biomedical Network Research; Centro de Investigación Biomédica En Red) is a public national consortium created in 2006 under the umbrella of the Spanish National Institute of Health Carlos III (ISCIII). This innovative research structure comprises 11 different specific areas dedicated to the main public health priorities in the National Health System. CIBERER, the thematic area of CIBER focused on rare diseases (RDs) currently consists of 75 research groups belonging to universities, research centers, and hospitals of the entire country. CIBERER's mission is to be a center prioritizing and favoring collaboration and cooperation between biomedical and clinical research groups, with special emphasis on the aspects of genetic, molecular, biochemical, and cellular research of RDs. This research is the basis for providing new tools for the diagnosis and therapy of low-prevalence diseases, in line with the International Rare Diseases Research Consortium (IRDiRC) objectives, thus favoring translational research between the scientific environment of the laboratory and the clinical setting of health centers. In this article, we intend to review CIBERER's 15-year journey and summarize the main results obtained in terms of internationalization, scientific production, contributions toward the discovery of new therapies and novel genes associated to diseases, cooperation with patients' associations and many other topics related to RD research
Estudi transcripcional i funcional de les ribonucleotidil reductases de Pseudomonas aeruginosa
[cat] bLes ribonucleotidil reductases (RNR) són metal·loenzims essencials per la vida que catalitzen la reducció dels ribonucleòtids (NTPs) a desoxiribonucleòtids (dNTPs), per tant, les RNRs són enzims necessaris per a l’obtenció dels precursors de la síntesi i reparació de l’ADN. Fins ara, s’han descrit tres classes de RNR que realitzen la mateixa reacció; la classe I (Ia, Ib i Ic), la classe II i la classe III. Totes tres classes de RNR tenen una estructura i una regulació al·lostèrica molt semblant, encara que els seus mecanismes d’activació o generació del radical són molt diferents. Els organismes eucariotes presenten un sol tipus de RNR, la classe Ia, però els bacteris codifiquen en el seu genoma per qualsevol classe de RNR, inclús, més d’una classe per tal de ser més flexibles i sobreviure en diferents condicions ambientals. Per exemple, el genoma del bacteri Pseudomonas aeruginosa codifica; la RNR de classe Ia (funcional en condicions aeròbiques), la classe II (funcional independentment de l’oxigen però depenent de la vitamina B12) i la classe III (funcional en condicions anaeròbiques estrictes). L’estudi de la regulació transcripcional d’aquest enzim serà clau per determinar l’expressió de cada classe de RNR en diferents condicions de creixement i doncs, evitar l’expressió o activitat d’aquests enzims i poder inhibir la divisió cel·lular. El principal factor transcripcional que regula la transcripció de les diferents RNRs és NrdR, tot i així, fins ara no s’havia estudiat aquest factor de transcripció en un microorganisme que codifiqui en el mateix genoma per a les tres classes de RNR, com és P. aeruginosa. En aquesta tesi s’ha estudiat tant el factor de transcripció NrdR com altres factors de transcripció reguladors dels gens nrd en condicions d’anaerobiosi, biofilm o d’infecció. Els resultats obtinguts mostren la inhibició de totes tres classes de RNR a través de NrdR regulant els nivells d’expressió de cada gen en diferents condicions ambientals. A més, s’ha vist que NrdR pot regular altres gens diferents de nrd, com ara topA. S’ha estudiat un altre factor de transcripció, l’AlgR, el qual regula gens de la síntesi d’alginat i que participen en la virulència de P. aeruginosa. S’ha vist que l’AlgR indueix els gens de les RNRs de classe Ia i II en condicions d’estrès cel·lular i durant el procés de formació de biofilm. A més, s’ha vist que les RNRs de classe II i III són importants per la formació d’un biofilm madur on l’oxigen és limitant. A més, les RNRs de classe II i III s’indueixen en condicions anaeròbies i en biofilm via el factor de transcripció Dnr. Sorprenentment, també s’ha observat que la soca P. aeruginosa PAO1 expressa menys el gen de la RNR de classe III que les soques de P. aeruginosa aïllades de pacients clínics, afectant el creixement anaeròbic i a la infecció de P. aeruginosa PAO1. Per tant, s’ha vist que la RNR de classe III és important per sintetitzar dNTP durant el procés de divisió cel·lular en una infecció. Per últim, s’han estudiat les condicions de síntesi de la vitamina B12 a P. aeruginosa. S’ha vist que la síntesi de la vitamina B12 a P. aeruginosa es troba induïda en condicions aeròbiques i durant el creixement en forma de biofilm, moment on la RNR de classe II és activa. Aquests resultats han aportat informació per entendre la reducció de ribonucleòtids a P. aeruginosa i doncs la divisió cel·lular d’aquesta, per tal de dissenyar, en un futur, una possible diana antimicrobiana.[eng] Ribonucleotide reductase (RNR) is an essential enzyme found in all life domains. The RNR catalyses the reduction of ribonucleotides to their corresponding deoxyribonucleotides (dNTP). These enzymes are involved in de novo synthesis of dNTPs, necessary for DNA synthesis and repair, so the balance of the different dNTP has to be carefully regulated. Therefore, RNR could be a target of antiviral, antibacterial and anti-cancer therapies. All known RNRs can be divided into three classes (I, II and III). Their differences are based on structure, metallocofactor requirements, and mechanisms used for radical generation. Interestingly, Pseudomonas aeruginosa, an opportunistic pathogen, is one of a few organisms that encodes in its genome three different classes (Ia, II and III) of the enzyme ribonucleotide reductase (RNR). Class I RNRs, encoded by the nrdA and nrdB genes, are found in both prokaryotic and eukaryotic organisms. The activity of class I RNR is restricted to aerobic conditions. Class II RNRs, encoded by the nrdJ gene, use vitamin B12 in the radical generation process, and operate both under aerobic and anaerobic conditions. This class has been found in archaea, eubacteria and some lower eukaryotes. Class III RNRs, encoded by the nrdD gene, can only operate under anaerobic conditions and has been found in archaea and eubacteria. In this work, we have identified different transcriptional factors of P. aeruginosa RNR. Particularly, we studied the NrdR in the transcriptional regulation of the different RNR genes during aerobic or anaerobic growth and its importance during infection. Furthermore we identified other transcriptional regulators important for the expression of RNR genes in anaerobic, biofilm and infection conditions (NarL, Dnr, AlgR…). Furthermore, we showed that the class II and III RNR are the most important RNR during biofilm formation. Surprisingly, we also demonstrated that P. aeruginosa PAO1 strain has difficulties to grow in anaerobic and infection conditions due to a mismatch in class III RNR promoter sequence. Finally, we demonstrated that P. aeruginosa syntheses vitamin B12 in aerobic and biofilm formation, determining the class II RNR activity. These results get us closer to understanding the regulation of complex RNR networks in P. aeruginosa, how it adapts to environmental conditions and evolves throughout its life cycle to design an antimicrobial compound
A global analysis of CNVs in swine using whole genome sequence data and association analysis with fatty acid composition and growth traits
Copy number variations (CNVs) are important genetic variants complementary to SNPs, and can be considered as biomarkers for some economically important traits in domestic animals. In the present study, a genomic analysis of porcine CNVs based on next-generation sequencing data was carried out to identify CNVs segregating in an Iberian x Landrace backcross population and study their association with fatty acid composition and growthrelated traits. A total of 1,279 CNVs, including duplications and deletions, were detected, ranging from 106 to 235 CNVs across samples, with an average of 183 CNVs per sample. Moreover, we detected 540 CNV regions (CNVRs) containing 245 genes. Functional annotation suggested that these genes possess a great variety of molecular functions and may play a role in production traits in commercial breeds. Some of the identified CNVRs contained relevant functional genes (e.g., CLCA4, CYP4X1, GPAT2, MOGAT2, PLA2G2A and PRKG1, among others). The variation in copy number of four of them (CLCA4, GPAT2, MOGAT2 and PRKG1) was validated in 150 BC1_LD (25% Iberian and 75% Landrace) animals by qPCR. Additionally, their contribution regarding backfat and intramuscular fatty acid composition and growth–related traits was analyzed. Statistically significant associations were obtained for CNVR112 (GPAT2) for the C18:2(n-6)/C18:3(n-3) ratio in backfat and carcass length, among others. Notably, GPATs are enzymes that catalyze the first step in the
biosynthesis of both triglycerides and glycerophospholipids, suggesting that this CNVR may contribute to genetic variation in fatty acid composition and growth traits. These findings provide useful genomic information to facilitate the further identification of trait-related CNVRs affecting economically important traits in pigs.info:eu-repo/semantics/publishedVersio
MOTEMO-OUTDOOR: Guaranteeing safety against COVID-19 through outdoor and e-learning teaching innovation experiences of active learning in higher education
The containment measures in the face of the COVID-19 epidemic have posed a notable challenge for formal teaching-learning processes, which have had to be adapted to a context of health security. An active learning program, MOTEMO-OUTDOOR was tested on a sample of 273 university undergraduate students. A within-subjects design was carried out with an adaptation of the four discussion seminars to three formats: face-to-face synchronous indoor (in a classroom), face-to-face synchronous outdoor (in a green space) and virtual asynchronous at home. Each student was assigned to the indoor (2 seminars) and outdoor (2 seminars) conditions, and a subsample (n = 30) also participated in the virtual context in application of the university's COVID lockdown protocols. The impact of the experience was evaluated in 6 dimensions (learning experience, evaluative impact, hedonic experience, technical conditions, environmental conditions and security against COVID-19). The exploratory factor analysis revealed a structure of two higher-order factors, called learning experience and learning conditions.The results relative to the general sample revealed a higher learning experience in the outdoor compared to the indoor context, being the dimension of hedonic experience the one that supposes the greatest difference between both.In contrast, the outdoor context presented better scores in learning conditions, with the component of environmental conditions being the one that supposed a greater difference between both.The analysis of the subsample revealed the absence of differences in the learning experience between the face-to-face vs. virtual contexts, despite the fact that the latter had better scores in the learning context factor with moderate effect sizes. It is concluded that this adaptation through active methodologies to an outdoor context and a virtual context, allows to overcome part of the technical and environmental limitations and improves health security perception, guaranteeing the learning experience, and thus provide with versatility the teaching-learning processes in a higher education context