Dolphin and whale: development, evaluation and application of novel bioinformatics tools for metabolite profiling in high throughput 1H-NMR analysis

El perfilat de metabòlits es la tasca més difícil dins l'anàlisi espectral de RMN. El seu objectiu es comprendre els processos biològics que tenen lloc en un moment concret mitjançant la identificació i quantificació dels metabòlits presents en mescles d' RMN complexes. Un espectre de RMN està compost per ressonàncies d'un gran nombre de metabòlits, i aquestes se solen solapar entre elles, canviar de posició depenent del pH de la mostra i poden quedar emmascarades per senyals de macromolècules. Tots aquests problemes compliquen la identificació i quantificació de metabòlits, pel que obtenir un perfil de metabòlits curat en una mostra pot ser un gran repte inclús per usuaris experts. En aquest context, la motivació d'aquesta tesi va néixer amb l'objectiu de donar automatismes i funcions fàcils de fer servir per al perfilat de metabòlits en RMN, millorant la qualitat dels resultats i reduint el temps d'anàlisi. Per fer-ho, es van implementar un conjunt d'algoritmes que van acabar empaquetats en dos programes, Dolphin i Whale.El perfilado de metabolitos es la tarea más difícil dentro del análisis espectral de RMN. Su objetivo es comprender los procesos biológicos que tienen lugar en un momento concreto a través de la identificación y cuantificación de los metabolitos presentes en mezclas de RMN complejas. Un espectro de RMN está compuesto por resonancias de un gran numero de metabolitos, y éstas a menudo se solapan entre ellas, cambian de posición dependiendo del pH de la muestra y pueden quedar enmascaradas por señales de macromoléculas. Todos estos problemas complican la identificación y cuantificación de metabolitos, por lo que obtener un perfilado de metabolitos curado en una muestra puede ser un gran reto incluso para usuarios expertos. En este contexto, la motivación de esta tesis nació con el objetivo de dar automatismos y funciones fáciles de usar para el perfilado de metabolitos en RMN, mejorando la calidad de los resultados y reduciendo el tiempo de análisis. Para hacerlo, se implementaron un conjunto de algoritmos que acabaron empaquetados en dos programas, Dolphin y Whale.Metabolite profiling is the most challenging approach in NMR spectral analysis. It aims to comprehend biological processes occurring in a certain moment through identifying and quantifying metabolites present in complex NMR mixtures. An NMR spectrum is composed by resonances of a huge number of metabolites, and these resonances often overlap between them, shift position depending on the sample pH and can be masked by macromolecules signals. All these drawbacks hinder metabolite identification and quantification, so obtaining a cured metabolite profile of a sample can be a very big issue even for expert users. In this context, the motivation of this thesis was born with the aim to provide automatisms and user-friendly interactive functions for NMR metabolite profiling, improving the quality of the results and reducing the time span of the analysis. To do so, several algorisms were implemented and embedded into two software packages, Dolphin and Whale

Protocol de vigilància epidemiològica per a la prevenció i el control de l’hepatitis C

Hepatitis C; Malalties transmissibles; PrevencióHepatitis C; Enfermedades trasmisibles; PrevenciónHepatitis C; Communicable diseases; PreventionProtocolo de actuación dirigido a los profesionales de la salud para el control y la prevención de la hepatitits CProtocol d'actuació dirigit als professionals de la salut per al control i la prevenció de l'hepatitis CProtocol of action aimed at health professionals to the control and prevention of hepatitis

Anàlisi electromiogràfica i de percepció d’esforç del tirant de musculació respecte de l’exercici de mig esquat

L’objectiu d’aquest estudi ha estat comparar l’exercici de flexió-extensió del genoll, realitzat amb el tirant de musculació (TM) amb l’exercici de mig esquat a diferents intensitats, a més a més de la percepció d’esforç dels subjectes en cadascun. Amb aquesta finalitat es van escollir 12 subjectes actius, de sexe masculí, als quals se’ls van realitzar registres electromiogràfics del vast extern del quàdriceps. Els resultats obtinguts suggereixen que no hi ha diferències significatives pel que fa a la resposta electromiogràfica i la percepció de l’esforç entre l’exercici realitzat sense càrrega extra mitjançant el TM i l’exercici de mig esquat al 50 % d’1 repetició màxima (1RM). Igualment, no es van trobar diferències significatives entre l’exercici amb TM i càrrega extra de 10 kg respecte de l’exercici de mig esquat amb càrrega extra de 60 % d’1RM i per a l’exercici amb TM i càrrega extra de 20 kg amb el mig esquat amb càrrega extra de 70 % d’1RM. Dels resultats obtinguts es deriva que l’exercici amb el TM pot ser una alternativa prou eficaç per a l’entrenament de força; entre els seus avantatges podem destacar-ne la facilitat d’ús, el baix cost econòmic i, sobretot, el fet de ser un mitjà d’entrenament que pot evitar lesions, perquè no li calen càrregues externes excessivament elevades

N=N Bond Cleavage by Tantalum Hydride Complexes: Mechanistic Insights and Reactivity.

A series of dinuclear tantalum(IV) hydrides [{TaCpRX2}2(mu-H)2] (CpR = eta5-C5Me5, eta5-C5H4SiMe3, eta5-C5HMe4; X = Cl, Br) show the ability to promote the N=N bond cleavage in their reactions with azobenzene and benzo[c]cinnoline in absence of reducing reagents. Both, characterization of intermediate species and DFT studies point to a mechanism in two stages, in which the Ta-Ta bond splitting is key for the reduction of the N=N bond and its complete scission.Consorcio Madroño - Universidad de Alcal

A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus)

Background: Genomic resources for plant and animal species that are under exploitation primarily for human consumption are increasingly important, among other things, for understanding physiological processes and for establishing adequate genetic selection programs. Current available techniques for high-throughput sequencing have been implemented in a number of species, including fish, to obtain a proper description of the transcriptome. The objective of this study was to generate a comprehensive transcriptomic database in turbot, a highly priced farmed fish species in Europe, with potential expansion to other areas of the world, for which there are unsolved production bottlenecks, to understand better reproductive- and immune-related functions. This information is essential to implement marker assisted selection programs useful for the turbot industry. Results: Expressed sequence tags were generated by Sanger sequencing of cDNA libraries from different immunerelated tissues after several parasitic challenges. The resulting database (“Turbot 2 database”) was enlarged with sequences generated from a 454 sequencing run of brain-hypophysis-gonadal axis-derived RNA obtained from turbot at different development stages. The assembly of Sanger and 454 sequences generated 52,427 consensus sequences (“Turbot 3 database”), of which 23,661 were successfully annotated. A total of 1,410 sequences were confirmed to be related to reproduction and key genes involved in sex differentiation and maturation were identified for the first time in turbot (AR, AMH, SRY-related genes, CYP19A, ZPGs, STAR FSHR, etc.). Similarly, 2,241 sequences were related to the immune system and several novel key immune genes were identified (BCL, TRAF, NCK, CD28 and TOLLIP, among others). The number of genes of many relevant reproduction- and immune-related pathways present in the database was 50–90% of the total gene count of each pathway. In addition, 1,237 microsatellites and 7,362 single nucleotide polymorphisms (SNPs) were also compiled. Further, 2,976 putative natural antisense transcripts (NATs) including microRNAs were also identified Conclusions: The combined sequencing strategies employed here significantly increased the turbot genomic resources available, including 34,400 novel sequences. The generated database contains a larger number of genes relevant for reproduction- and immune-associated studies, with an excellent coverage of most genes present in many relevant physiological pathways. This database also allowed the identification of many microsatellites and SNP markers that will be very useful for population and genome screening and a valuable aid in marker assisted selection programs.The current work was granted by the Spanish Government thanks to a Consolider Project (Project Aquagenomics, ref. CDS2007-0002) and to projects AGL2006-13158-C03 and AGL2009-13282-C01 and C02. LR was supported by an Aquagenomics postdoctoral contract and BGP was supported by an Isidro Parga Pondal research fellowship from the Xunta de Galicia (Spain).S

Análisis electromiográfico y de percepción de esfuerzo del tirante musculador con respecto al ejercicio de medio squat

El objetivo del presente estudio ha sido comparar el ejercicio de flexo-extensión de la rodilla realizado con el tirante musculador  (TM) con el ejercicio de medio squat a distintas intensidades, además de la percepción de esfuerzo de los sujetos en cada uno de ellos. Con tal finalidad se eligieron 12 sujetos activos del sexo masculino a los que se les realizaron registros electromiográficos del vasto externo del cuadriceps. Los resultados obtenidos sugieren que no hay diferencias significativas en cuanto a respuesta electromiográfica y percepción del esfuerza entre el ejercicio realizado sin carga extra mediante el TM y el ejercicio de medio squat al 50 % de 1 repetición máxima (1RM). De igual modo no se hallaron diferencias significativas entre el ejercicio con TM y carga extra de 10 kg con respecto al ejercicio de medio squat con carga extra de 60 % de 1RM y para el ejercicio con TM y carga extra de 20 kg con el medio squat con carga extra de 70 % de 1 RM.  De los resultados obtenidos se deriva que el ejercicio con el TM puede ser una alternativa bastante eficaz para el entrenamiento de fuerza; entre sus ventajas podemos destacar su facilidad de uso, bajo costo económico y, sobre todo, el hecho de poder ser un medio de entrenamiento que pueda evitar lesiones al no precisar de cargas externas exc esivamente elevadas

V232D Mutation in Patients With Cystic Fibrosis: Not So Rare, Not So Mild

The frequency of some Cystic Fibrosis (CF) Transmembrane Conductance Regulator gene (CFTR) mutations varies between populations. Genetic testing during newborn screening (NBS) for CF can identify less common mutations with low clinical expression in childhood and previously considered mild but not fully characterized, such as the mutation p.Val232Asp (c.695T > A). The aim of this study was to describe CF patients with the V232D mutation. We identify CF children with the V232D mutation detected by NBS and compare them with CF adults with this mutation whose diagnosis was prompted by clinical symptoms in the same period. We studied clinical, biochemical, spirometric, and prognostic features in both populations. NBS program tested 276,523 children during a period of 14 years (2003-2017) and identified 54 cases of CF. Six children (11%) had the V232D mutation. Over the same period, 5 adults (age 37.6 ± 16.29 years old) with symptoms of CF and this mutation were also diagnosed. Follow-up duration was mean 10.1 years for adults and mean 6.5 years for children. In the adult group, lung function was impaired at diagnosis in all patients (Forced Expiratory Volume1-FEV1-67.12% ± 13.09) and worsened in children tested during evolution (FEV1first: 113%; FEV1last: 64%). Pancreatic insufficiency was present in adult group, with recurrent pancreatitis in 1 present. Although with less clinical expression in children, V232D is associated with pulmonary and pancreatic involvement during adulthood and CF cannot be considered mild. This mutation is present in 11% of all patients diagnosed with CF in our region. Its inclusion in some NBS programs should be taken into account in order to improve the prognosis of affected children.S

Nolz1 promotes striatal neurogenesis through the regulation of retinoic acid signaling

Background: Nolz1 is a zinc finger transcription factor whose expression is enriched in the lateral ganglionic eminence (LGE), although its function is still unknown. Results: Here we analyze the role of Nolz1 during LGE development. We show that Nolz1 expression is high in proliferating neural progenitor cells (NPCs) of the LGE subventricular zone. In addition, low levels of Nolz1 are detected in the mantle zone, as well as in the adult striatum. Similarly, Nolz1 is highly expressed in proliferating LGE-derived NPC cultures, but its levels rapidly decrease upon cell differentiation, pointing to a role of Nolz1 in the control of NPC proliferation and/or differentiation. In agreement with this hypothesis, we find that Nolz1 over-expression promotes cell cycle exit of NPCs in neurosphere cultures and negatively regulates proliferation in telencephalic organotypic cultures. Within LGE primary cultures, Nolz1 over-expression promotes the acquisition of a neuronal phenotype, since it increases the number of β-III tubulin (Tuj1)- and microtubule-associated protein (MAP)2-positive neurons, and inhibits astrocyte generation and/or differentiation. Retinoic acid (RA) is one of the most important morphogens involved in striatal neurogenesis, and regulates Nolz1 expression in different systems. Here we show that Nolz1 also responds to this morphogen in E12.5 LGE-derived cell cultures. However, Nolz1 expression is not regulated by RA in E14.5 LGE-derived cell cultures, nor is it affected during LGE development in mouse models that present decreased RA levels. Interestingly, we find that Gsx2, which is necessary for normal RA signaling during LGE development, is also required for Nolz1 expression, which is lost in Gsx2 knockout mice. These findings suggest that Nolz1 might act downstream of Gsx2 to regulate RA-induced neurogenesis. Keeping with this hypothesis, we show that Nolz1 induces the selective expression of the RA receptor (RAR)β without altering RARα or RARγ. In addition, Nozl1 over-expression increases RA signaling since it stimulates the RA response element. This RA signaling is essential for Nolz1-induced neurogenesis, which is impaired in a RA-free environment or in the presence of a RAR inverse agonist. It has been proposed that Drosophila Gsx2 and Nolz1 homologues could cooperate with the transcriptional co-repressors Groucho-TLE to regulate cell proliferation. In agreement with this view, we show that Nolz1 could act in collaboration with TLE-4, as they are expressed at the same time in NPC cultures and during mouse development. Conclusions: Nolz1 promotes RA signaling in the LGE, contributing to the striatal neurogenesis during development

One-year cardiovascular outcomes after coronavirus disease 2019: The cardiovascular COVID-19 registry

Background: The long-term cardiovascular (CV) outcomes of COVID-19 have not been fully explored. Methods: This was an international, multicenter, retrospective cohort study conducted between February and December 2020. Consecutive patients ?18 years who underwent a real-time reverse transcriptase-polymerase chain reaction (RT-PCR) for SARS-CoV2 were included. Patients were classified into two cohorts depending on the nasopharyngeal swab result and clinical status: confirmed COVID-19 (positive RT-PCR) and control (without suggestive symptoms and negative RT-PCR). Data were obtained from electronic records, and clinical follow-up was performed at 1-year. The primary outcome was CV death at 1-year. Secondary outcomes included arterial thrombotic events (ATE), venous thromboembolism (VTE), and serious cardiac arrhythmias. An independent clinical event committee adjudicated events. A Cox proportional hazards model adjusted for all baseline characteristics was used for comparing outcomes between groups. A prespecified landmark analysis was performed to assess events during the post-acute phase (31-365 days). Results: A total of 4,427 patients were included: 3,578 (80.8%) in the COVID-19 and 849 (19.2%) control cohorts. At one year, there were no significant differences in the primary endpoint of CV death between the COVID-19 and control cohorts (1.4% vs. 0.8%; HRadj 1.28 [0.56-2.91]; p = 0.555), but there was a higher risk of all-cause death (17.8% vs. 4.0%; HRadj 2.82 [1.99-4.0]; p = 0.001). COVID-19 cohort had higher rates of ATE (2.5% vs. 0.8%, HRadj 2.26 [1.02-4.99]; p = 0.044), VTE (3.7% vs. 0.4%, HRadj 9.33 [2.93-29.70]; p = 0.001), and serious cardiac arrhythmias (2.5% vs. 0.6%, HRadj 3.37 [1.35-8.46]; p = 0.010). During the post-acute phase, there were no significant differences in CV death (0.6% vs. 0.7%; HRadj 0.67 [0.25-1.80]; p = 0.425), but there was a higher risk of deep vein thrombosis (0.6% vs. 0.0%; p = 0.028). Re-hospitalization rate was lower in the COVID-19 cohort compared to the control cohort (13.9% vs. 20.6%; p = 0.001). Conclusions: At 1-year, patients with COVID-19 experienced an increased risk of all-cause death and adverse CV events, including ATE, VTE, and serious cardiac arrhythmias, but not CV death