Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX

<p>Abstract</p> <p>Background</p> <p>The Distributed Annotation System (DAS) is a widely used network protocol for sharing biological information. The distributed aspects of the protocol enable the use of various reference and annotation servers for connecting biological sequence data to pertinent annotations in order to depict an integrated view of the data for the final user.</p> <p>Results</p> <p>An annotation server has been devised to provide information about the endogenous retroviruses detected and annotated by a specialized <it>in silico </it>tool called RetroTector. We describe the procedure to implement the DAS 1.5 protocol commands necessary for constructing the DAS annotation server. We use our server to exemplify those steps. Data distribution is kept separated from visualization which is carried out by eBioX, an easy to use open source program incorporating multiple bioinformatics utilities. Some well characterized endogenous retroviruses are shown in two different DAS clients. A rapid analysis of areas free from retroviral insertions could be facilitated by our annotations.</p> <p>Conclusion</p> <p>The DAS protocol has shown to be advantageous in the distribution of endogenous retrovirus data. The distributed nature of the protocol is also found to aid in combining annotation and visualization along a genome in order to enhance the understanding of ERV contribution to its evolution. Reference and annotation servers are conjointly used by eBioX to provide visualization of ERV annotations as well as other data sources. Our DAS data source can be found in the central public DAS service repository, <url>http://www.dasregistry.org</url>, or at <url>http://loka.bmc.uu.se/das/sources</url>.</p

La renovación de contenidos en asignaturas de comunicación y su impacto en el marco emocional del aprendizaje: un caso de estudio en narrativa audiovisual.

Este artículo analiza las bases y la evolución de la Narrativa Audiovisual como asignatura fundamental de la carrera de comunicación audiovisual. Es el resultado de un proyecto de investigación orientado hacia un replanteamiento general de las asignaturas universitarias, que trata de investigar la docencia y sus resultados, a la vez que pretende introducir un nuevo paradigma centrado en el ser humano. Se analizan los marcos de referencia más habituales y se propone un nuevo planteamiento.This paper analyzes the foundations and evolution of Storytelling as a fundamental subject in Communication university degree programs. It is the result of a research project focused on a general rethinking of university subjects, which is teaching and research results as well as to introduce a new paradigm centered on the human being. The most common reference frames are discussed and a new approach is proposed.post-print337 K

Dynamics of excitable cells: spike-adding phenomena in action

We study the dynamics of action potentials of some electrically excitable cells: neurons and cardiac muscle cells. Bursting, following a fast–slow dynamics, is the most characteristic behavior of these dynamical systems, and the number of spikes may change due to spike-adding phenomenon. Using analytical and numerical methods we give, by focusing on the paradigmatic 3D Hindmarsh–Rose neuron model, a review of recent results on the global organization of the parameter space of neuron models with bursting regions occurring between saddle-node and homoclinic bifurcations (fold/hom bursting). We provide a generic overview of the different bursting regimes that appear in the parametric phase space of the model and the bifurcations among them. These techniques are applied in two realistic frameworks: insect movement gait changes and the appearance of Early Afterdepolarizations in cardiac dynamics

Proteomic Study of the Interactions between Phages and the Bacterial Host Klebsiella pneumoniae

Phages and bacteria have acquired resistance mechanisms for protection. In this context, the aims of the present study were to analyze the proteins isolated from 21 novel lytic phages of Klebsiella pneumoniae in search of defense mechanisms against bacteria and also to determine the infective capacity of the phages. A proteomic study was also conducted to investigate the defense mechanisms of two clinical isolates of K. pneumoniae infected by phages. For this purpose, the 21 lytic phages were sequenced and de novo assembled. The host range was determined in a collection of 47 clinical isolates of K. pneumoniae, revealing the variable infective capacity of the phages. Genome sequencing showed that all of the phages were lytic phages belonging to the order Caudovirales. Phage sequence analysis revealed that the proteins were organized in functional modules within the genome. Although most of the proteins have unknown functions, multiple proteins were associated with defense mechanisms against bacteria, including the restriction-modification system, the toxin-antitoxin system, evasion of DNA degradation, blocking of host restriction and modification, the orphan CRISPR-Cas system, and the anti-CRISPR system. Proteomic study of the phage-host interactions (i.e., between isolates K3574 and K3320, which have intact CRISPR-Cas systems, and phages vB_KpnS-VAC35 and vB_KpnM-VAC36, respectively) revealed the presence of several defense mechanisms against phage infection (prophage, defense/virulence/resistance, oxidative stress and plasmid proteins) in the bacteria, and of the Acr candidate (anti-CRISPR protein) in the phages. IMPORTANCE Researchers, including microbiologists and infectious disease specialists, require more knowledge about the interactions between phages and their bacterial hosts and about their defense mechanisms. In this study, we analyzed the molecular mechanisms of viral and bacterial defense in phages infecting clinical isolates of K. pneumoniae. Viral defense mechanisms included restriction-modification system evasion, the toxin-antitoxin (TA) system, DNA degradation evasion, blocking of host restriction and modification, and resistance to the abortive infection system, anti-CRISPR and CRISPR-Cas systems. Regarding bacterial defense mechanisms, proteomic analysis revealed expression of proteins involved in the prophage (FtsH protease modulator), plasmid (cupin phosphomannose isomerase protein), defense/virulence/resistance (porins, efflux pumps, lipopolysaccharide, pilus elements, quorum network proteins, TA systems, and methyltransferases), oxidative stress mechanisms, and Acr candidates (anti-CRISPR protein). The findings reveal some important molecular mechanisms involved in the phage-host bacterial interactions; however, further study in this field is required to improve the efficacy of phage therapy.This study was funded by grant PI19/00878 and PI22/00323 awarded to M.T. within the State Plan for R1D1I 2013-2016 (National Plan for Scientific Research, Technological Development, and Innovation 2008-2011) and cofinanced by the ISCIII-Deputy General Directorate for Evaluation and Promotion of Research/European Regional Development Fund “A Way of Making Europe” and Instituto de Salud Carlos III FEDER, Spanish Network for the Research in Infectious Diseases (REIPI; RD16/0016/0006 and RD16/0016/0008), CIBERINFEC (CIBER21/13/00012, CB21/13/00049, CIBER21/13/00084, and CIBER21/13/00095), and Personalized Medicine Project (MePRAM; PMP/00092) and also by the Study Group on Mechanisms of Action and Resistance to Antimicrobials, GEMARA (SEIMC; http://www.seimc.org/). M.T. was financially supported by the Miguel Servet Research Program (SERGAS and ISCIII). I.B. was financially supported by pFIS program (ISCIII, FI20/00302). O.P., L.F.-G., and M.L. were financially supported by grants IN606A-2020/035, IN606B-2021/013, and IN606C-2022/002, respectively (GAIN; Xunta de Galicia). The authors acknowledge CESGA (www.cesga.es) in Santiago de Compostela, Spain, for providing access to computing facilities and the RIAIDT-USC analytical facilities. Finally, We thank researchers from the Spanish Network of Bacteriophages and Transducer Elements (FAGOMA) for contributing the lytic phages. I.B., L.B., O.P., and L.F.-G. developed the experiments, analyzed the results, and wrote the original manuscript. M.L., C.O.C. and A.B.P. helped to prepare the visual presentation of the results. F.F.C., Á.P., L.M.-M., and J.O.-I. rewrote the manuscript. M.T. financed and directed the experiments and supervised the writing of the originalmanuscript. We declare that there are no conflicts of interest.S

The medieval town of Handoga (Djibouti): A report of the 2021 field season

The article presents the results of the first campaign carried out at the medieval site of Handoga (Djibouti) by the StateHorn project, based at the Institute of Heritage Sciences of the Spanish National Research Council. The aim of the campaign was to assess the site's potential in order to launch a long-term project focusing on the study of the town's urbanism and way of life. The campaign included a systematic survey of the site and the excavation of four test pits, which revealed evidence for two archaeological phases at Handoga. The results of the campaign suggest that Handoga was an important urban centre on the medieval routes linking the Gulf of Tadjoura with the interior of Africa, of which very little is known

Alteration of medial-edge epithelium cell adhesion in two Tgf-β3 null mouse strains

Although palatal shelf adhesion is a crucial event during palate development, little work has been carried out to determine which molecules are responsible for this process. Furthermore, whether altered palatal shelf adhesion causes the cleft palate presented by Tgf-β3 null mutant mice has not yet been clarified. Here, we study the presence/distribution of some extracellular matrix and cell adhesion molecules at the time of the contact of palatal shelves in both wild-type and Tgf-β3 null mutant palates of two strains of mice (C57/BL/6J (C57), and MF1) that develop cleft palates of different severity. We have performed immunohistochemistry with antibodies against collagens IV and IX, laminin, fibronectin, the α5- and β1-integrins, and ICAM-1; in situ hybridization with a Nectin-1 riboprobe; and palatal shelf cultures treated or untreated with TGF-β3 or neutralizing antibodies against fibronectin or the α5-integrin. Our results show the location of these molecules in the wild-type mouse medial edge epithelium (MEE) of both strains at the time of the contact of palatal shelves; the heavier (C57) and milder (MF1) alteration of their presence in the Tgf-β3 null mutants; the importance of TGF-β3 to restore their normal pattern of expression; and the crucial role of fibronectin and the α5-integrin in palatal shelf adhesion. We thus provide insight into the molecular bases of this important process and the cleft palate presented by Tgf-β3 null mutant mice

The First Sequenced Carnivore Genome Shows Complex Host-Endogenous Retrovirus Relationships

Host-retrovirus interactions influence the genomic landscape and have contributed substantially to mammalian genome evolution. To gain further insights, we analyzed a female boxer (Canis familiaris) genome for complexity and integration pattern of canine endogenous retroviruses (CfERV). Intriguingly, the first such in-depth analysis of a carnivore species identified 407 CfERV proviruses that represent only 0.15% of the dog genome. In comparison, the same detection criteria identified about six times more HERV proviruses in the human genome that has been estimated to contain a total of 8% retroviral DNA including solitary LTRs. These observed differences in man and dog are likely due to different mechanisms to purge, restrict and protect their genomes against retroviruses. A novel group of gammaretrovirus-like CfERV with high similarity to HERV-Fc1 was found to have potential for active retrotransposition and possibly lateral transmissions between dog and human as a result of close interactions during at least 10.000 years. The CfERV integration landscape showed a non-uniform intra- and inter-chromosomal distribution. Like in other species, different densities of ERVs were observed. Some chromosomal regions were essentially devoid of CfERVs whereas other regions had large numbers of integrations in agreement with distinct selective pressures at different loci. Most CfERVs were integrated in antisense orientation within 100 kb from annotated protein-coding genes. This integration pattern provides evidence for selection against CfERVs in sense orientation relative to chromosomal genes. In conclusion, this ERV analysis of the first carnivorous species supports the notion that different mammals interact distinctively with endogenous retroviruses and suggests that retroviral lateral transmissions between dog and human may have occurred

Correction : Chaparro et al. Incidence, Clinical Characteristics and Management of Inflammatory Bowel Disease in Spain: Large-Scale Epidemiological Study. J. Clin. Med. 2021, 10, 2885

The authors wish to make the following corrections to this paper [...]

Incidence, Clinical Characteristics and Management of Inflammatory Bowel Disease in Spain : Large-Scale Epidemiological Study

(1) Aims: To assess the incidence of inflammatory bowel disease (IBD) in Spain, to describe the main epidemiological and clinical characteristics at diagnosis and the evolution of the disease, and to explore the use of drug treatments. (2) Methods: Prospective, population-based nationwide registry. Adult patients diagnosed with IBD-Crohn's disease (CD), ulcerative colitis (UC) or IBD unclassified (IBD-U)-during 2017 in Spain were included and were followed-up for 1 year. (3) Results: We identified 3611 incident cases of IBD diagnosed during 2017 in 108 hospitals covering over 22 million inhabitants. The overall incidence (cases/100,000 person-years) was 16 for IBD, 7.5 for CD, 8 for UC, and 0.5 for IBD-U; 53% of patients were male and median age was 43 years (interquartile range = 31-56 years). During a median 12-month follow-up, 34% of patients were treated with systemic steroids, 25% with immunomodulators, 15% with biologics and 5.6% underwent surgery. The percentage of patients under these treatments was significantly higher in CD than UC and IBD-U. Use of systemic steroids and biologics was significantly higher in hospitals with high resources. In total, 28% of patients were hospitalized (35% CD and 22% UC patients, p < 0.01). (4) Conclusion: The incidence of IBD in Spain is rather high and similar to that reported in Northern Europe. IBD patients require substantial therapeutic resources, which are greater in CD and in hospitals with high resources, and much higher than previously reported. One third of patients are hospitalized in the first year after diagnosis and a relevant proportion undergo surgery