Aplicaciones de software libre para docencia en ingeniería

Póster presentado en: VIII Jornadas de Innovación Docente de la UBU, Burgos, 5 de abril de 2016, organizadas por el Instituto de Formación e Innovación Educativa-IFIE de la Universidad de Burgo

Laboratorios virtuales y experimentos simulados para innovación docente

Póster presentado en: VIII Jornadas de Innovación Docente de la UBU, Burgos, 5 de abril de 2016, organizadas por el Instituto de Formación e Innovación Educativa-IFIE de la Universidad de Burgo

Programas de visualización 3D y servidores web de predicción de estructuras para la enseñanza en biotecnología

Póster presentado en: VIII Jornadas de Innovación Docente de la UBU, Burgos, 5 de abril de 2016, organizadas por el Instituto de Formación e Innovación Educativa-IFIE de la Universidad de Burgo

Colonization of electrospun polycaprolactone fibers by relevant pathogenic bacterial strains

Electrospun biodegradable polymers have emerged as promising materials for their applications in several fields, including biomedicine and food industry. For this reason, the susceptibility of these materials to be colonized by different pathogens is a critical issue for public health, and their study can provide future knowledge to develop new strategies against bacterial infections. In this work, the ability of three pathogenic bacterial species (Pseudomonas aeruginosa, Acinetobacter baumannii, and Listeria monocytogenes) to adhere and form biofilm in electrospun polycaprolactone (PCL) microfibrous meshes was investigated. Bacterial attachment was analyzed in meshes with different microstructure, and comparisons with other materials (borosilicate glass and electrospun polylactic acid (PLA)) fibers were assessed. Analysis included colony forming unit (CFU) counts, scanning electron microscopy (SEM), and crystal violet (CV) staining. All the obtained data suggest that PCL meshes, regardless of their microstructure, are highly susceptible to be colonized by the pathogenic relevant bacteria used in this study, so a pretreatment or a functionalization with compounds that present some antimicrobial activity or antibiofilm properties is highly recommended before their application. Moreover, an experiment designed to simulate a chronic wound environment was used to demonstrate the ability of these meshes to detach biofilms from the substratum where they have developed, thus making them promising candidates to be used in wound cleaning and disinfection.European Union’s H2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 691095 and Junta de Castilla y Leon-FEDER (projects BU079U16 and BU092U16)

Kinky DNA in solution: Small-angle-scattering study of a nucleosome positioning sequence

DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of lp ≈ 500Å is inconsistent with recent studies on short-chain DNA that show much greater flexibility but do not probe its origin. We have performed x-ray and neutron small-angle scattering on a short DNA sequence containing a strong nucleosome positioning element and analyzed the results using a modified Kratky-Porod model to determine possible conformations. Our results support a hypothesis from Crick and Klug in 1975 that some DNA sequences in solution can have sharp kinks, potentially resolving the discrepancy. Our conclusions are supported by measurements on a radiation-damaged sample, where single-strand breaks lead to increased flexibility and by an analysis of data from another sequence, which does not have kinks, but where our method can detect a locally enhanced flexibility due to an AT domain.Spanish Ministry of Economy, Industry and Competitiveness (BES-2013-065453, EEBB-I-2015-09973, FIS2012-38827). S.C.L. and UC-154 are grateful for the support of Junta de Castilla y Leon (Spain) Nanofibersafe BU079U16. D.A. acknowledges funding from the Agence Nationale de la Recherche through ANR-12-BSV5-0017-01 “Chrome” and ANR-17-CE11-0019-03 “Chrom3D” grants. N.T. acknowledges support by the project Advanced Materials and Devices (MIS 5002409, Competitiveness, Entrepreneurship and Innovation, NSRF 2014-2020) cofinanced by Greece and the European Regional Development Fund

Nonsense-mediated mRNA decay controls the changes in yeast ribosomal protein pre-mRNAs levels upon osmotic stress

The expression of ribosomal protein (RP) genes requires a substantial part of cellular transcription, processing and translation resources. Thus, the RP expression must be tightly regulated in response to conditions that compromise cell survival. In Saccharomyces cerevisiae cells, regulation of the RP gene expression at the transcriptional, mature mRNA stability and translational levels during the response to osmotic stress has been reported. Reprogramming global protein synthesis upon osmotic shock includes the movement of ribosomes from RP transcripts to stress-induced mRNAs. Using tiling arrays, we show that osmotic stress yields a drop in the levels of RP pre-mRNAs in S. cerevisiae cells. An analysis of the tiling array data, together with transcription rates data, shows a poor correlation, indicating that the drop in the RP pre-mRNA levels is not merely a result of the lowered RP transcription rates. A kinetic study using quantitative RT-PCR confirmed the decrease in the levels of several RP-unspliced transcripts during the first 15 minutes of osmotic stress, which seems independent of MAP kinase Hog1. Moreover, we found that the mutations in the components of the nonsense-mediated mRNA decay (NMD), Upf1, Upf2, Upf3 or in exonuclease Xrn1, eliminate the osmotic stress-induced drop in RP pre-mRNAs. Altogether, our results indicate that the degradation of yeast RP unspliced transcripts by NMD increases during osmotic stress, and suggest that this might be another mechanism to control RP synthesis during the stress response

Spatiotemporal Characteristics of the Largest HIV-1 CRF02_AG Outbreak in Spain: Evidence for Onward Transmissions

Background and Aim: The circulating recombinant form 02_AG (CRF02_AG) is the predominant clade among the human immunodeficiency virus type-1 (HIV-1) non-Bs with a prevalence of 5.97% (95% Confidence Interval-CI: 5.41–6.57%) across Spain. Our aim was to estimate the levels of regional clustering for CRF02_AG and the spatiotemporal characteristics of the largest CRF02_AG subepidemic in Spain.Methods: We studied 396 CRF02_AG sequences obtained from HIV-1 diagnosed patients during 2000–2014 from 10 autonomous communities of Spain. Phylogenetic analysis was performed on the 391 CRF02_AG sequences along with all globally sampled CRF02_AG sequences (N = 3,302) as references. Phylodynamic and phylogeographic analysis was performed to the largest CRF02_AG monophyletic cluster by a Bayesian method in BEAST v1.8.0 and by reconstructing ancestral states using the criterion of parsimony in Mesquite v3.4, respectively.Results: The HIV-1 CRF02_AG prevalence differed across Spanish autonomous communities we sampled from (p < 0.001). Phylogenetic analysis revealed that 52.7% of the CRF02_AG sequences formed 56 monophyletic clusters, with a range of 2–79 sequences. The CRF02_AG regional dispersal differed across Spain (p = 0.003), as suggested by monophyletic clustering. For the largest monophyletic cluster (subepidemic) (N = 79), 49.4% of the clustered sequences originated from Madrid, while most sequences (51.9%) had been obtained from men having sex with men (MSM). Molecular clock analysis suggested that the origin (tMRCA) of the CRF02_AG subepidemic was in 2002 (median estimate; 95% Highest Posterior Density-HPD interval: 1999–2004). Additionally, we found significant clustering within the CRF02_AG subepidemic according to the ethnic origin.Conclusion: CRF02_AG has been introduced as a result of multiple introductions in Spain, following regional dispersal in several cases. We showed that CRF02_AG transmissions were mostly due to regional dispersal in Spain. The hot-spot for the largest CRF02_AG regional subepidemic in Spain was in Madrid associated with MSM transmission risk group. The existence of subepidemics suggest that several spillovers occurred from Madrid to other areas. CRF02_AG sequences from Hispanics were clustered in a separate subclade suggesting no linkage between the local and Hispanic subepidemics

Specific and global regulation of mRNA stability during osmotic stress in Saccharomyces cerevisiae

Hyperosmotic stress yields reprogramming of gene expression in Saccharomyces cerevisiae cells. Most of this response is orchestrated by Hog1, a stress-activated, mitogen-activated protein kinase (MAPK) homologous to human p38. We investigated, on a genomic scale, the contribution of changes in transcription rates and mRNA stabilities to the modulation of mRNA amounts during the response to osmotic stress in wild-type and hog1 mutant cells. Mild osmotic shock induces a broad mRNA destabilization; however, osmo-mRNAs are up-regulated by increasing both transcription rates and mRNA half-lives. In contrast, mild or severe osmotic stress in hog1 mutants, or severe osmotic stress in wild-type cells, yields global mRNA stabilization and sequestration of mRNAs into P-bodies. After adaptation, the absence of Hog1 affects the kinetics of P-bodies disassembly and the return of mRNAs to translation. Our results indicate that regulation of mRNA turnover contributes to coordinate gene expression upon osmotic stress, and that there are both specific and global controls of mRNA stability depending on the strength of the osmotic stress

Analysis of Polycaprolactone Microfibers as Biofilm Carriers for Biotechnologically Relevant Bacteria

Polymeric electrospun fibers are becoming popular in microbial biotechnology because of their exceptional physicochemical characteristics, biodegradability, surface-to-volume ratio, and compatibility with biological systems, which give them a great potential as microbial supports to be used in production processes or environmental applications. In this work, we analyzed and compared the ability of Escherichia coli, Pseudomonas putida, Brevundimonas diminuta, and Sphingobium fuliginis to develop biofilms on different types of polycaprolactone (PCL) microfibers. These bacterial species are relevant in the production of biobased chemicals, enzymes, and proteins for therapeutic use and bioremediation. The obtained results demonstrated that all selected species were able to attach efficiently to the PCL microfibers. Also, the ability of pure cultures of S. fuliginis (former Flavobacterium sp. ATCC 27551, a very relevant strain in the bioremediation of organophosphorus compounds) to form dense biofilms was observed for the first time, opening the possibility of new applications for this microorganism. This material showed to have a high microbial loading capacity, regardless of the mesh density and fiber diameter. A comparative analysis between PCL and polylactic acid (PLA) electrospun microfibers indicated that both surfaces have a similar bacterial loading capacity, but the former material showed higher resistance to microbial degradation than PLA.European Union’s H2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 691095. The contracts of J.A.T.-R. and C.R. were supported by the grant nos. BU079U16 and BU092U16, that were co-financed by Junta de Castilla y León and the European Social Fund