Alineamiento múltiple de secuencias con T-Coffee: una aproximación paralela

Las aplicaciones de alineamiento múltiple de secuencias son prototipos de aplicaciones que requieren elevada potencia de cómputo y memoria. Se destacan por la relevancia científica que tienen los resultados que brindan a investigaciones científicas en el campo de la biomedicina, genética y farmacología. Las aplicaciones de alineamiento múltiple tienen la limitante de que no son capaces de procesar miles de secuencias, por lo que se hace necesario crear un modelo para resolver la problemática. Analizando el volumen de datos que se manipulan en el área de las ciencias biológica y la complejidad de los algoritmos de alineamiento de secuencias, la única vía de solución del problema es a través de la utilización de entornos de cómputo paralelos y la computación de altas prestaciones. La investigación realizada por nosotros tiene como objetivo la creación de un modelo paralelo que le permita a los algoritmos de alineamiento múltiple aumentar el número de secuencias a procesar, tratando de mantener la calidad en los resultados para garantizar la precisión científica. El modelo que proponemos emplea como base la clusterización de las secuencias de entrada utilizando criterios biológicos que permiten mantener la calidad de los resultados. Además, el modelo se enfoca en la disminución del tiempo de cómputo y consumo de memoria. Para presentar y validar el modelo utilizamos T-Coffee, como plataforma de desarrollo e investigación. El modelo propuesto pudiera ser aplicado a cualquier otro algoritmo de alineamiento múltiple de secuencias.

Diagnosi ambiental de la riera de Santa Coloma entre Santa Coloma de Farners i Riudarenes

A l’actualitat trobem nombrosos sistemes aquàtics alterats per diferents efectes d’origen antropogènic. Per tal d’evitar i/o disminuir aquests efectes va sorgir la Directiva Marc de l’Aigua (2000/60/CE) essent aquest un dels seus objectius. Aquest article descriu el funcionament hidrogeològic i l’estat ecològic de la riera de Santa Coloma, afluent de la Tordera (NE Catalunya), des de pràcticament el seu inici a Santa Coloma de Farners (Girona) fins a Riudarenes (Girona). S’intenta establir les possibles influències del funcionament hidrogeològic en l’estat ecològic a partir de dades piezomètriques, de cabal, fisicoquímiques i biològiques. Per aquesta última part s’han utilitzat indicadors biològics com l’índex d’hàbitat fluvial (IHF), avaluant l’hàbitat físic; l’índex de Qualitat del Bosc de Ribera (QBR), per determinar la qualitat ecològica de la zona de ribera; l’índex Biological Monitorig Working Party per a conques internes de Catalunya (BMWPC), per avaluar les diferents famílies de macroinvertebrats que hi viuen i l’índex ECOSTRIMED, una síntesi dels dos índex anteriors.

Nuevas orientaciones en historia económica: innovaciones biológicas y cambio técnico, siglos XIX-XX

Las innovaciones biológicas han sido siempre consustanciales al desarrollo económico, pero no suelen ser consideradas en Historia Económica. En parte esta situación es consecuencia de la escasa información disponible de aquella variable, en relación con la clase de informaciones que historiadores y economistas estamos acostumbrados a utilizar. La escasa atención de la Historia Económica por las innovaciones biológicas también está relacionada con la marcada tendencia de sus especialistas a minimizar la importancia de los ciclos biológicos en el sector agrario. Por uno y otro motivo, cuando aquellos especialistas analizan por ejemplo los cambios técnicos en la agricultura, tienden a utilizar unos modelos de referencia más relacionados con aquellas otras actividades, donde la incidencia de los ciclos biológicos es menos evidente a corto plazo. Esta situación también afecta, aunque algo menos, a la Historia Agraria. Las anteriores deficiencias están muy presentes en la Historia Agraria europea. En la historiografía de Estados Unidos, en cambio, las innovaciones biológicas han sido más estudiadas, y las aportaciones que se han realizado en esta dirección son muy destacables.

Caracterización de biomarcadores en la recurrencia postquirúrgica de la enfermedad de Crohn: valor predictivo y/o implicación patogénica de los mismos

La recurrència postquirúrgica en els pacients amb malaltia de Crohn intervinguts és molt freqüent i, al seu torn, té implicacions terapèutiques importants. No s'han caracteritzat fins ara marcadors biològics que, pel seu valor predictiu, poguessin ser d'utilitat en el maneig postquirúrgic d'aquests pacients. En aquest estudi s'analitza el perfil evolutiu després de la cirurgia de diverses citocines (IL-2, IL-6, IL-10, IL1B, IFN-g i TNF-a), marcadors fecals (calprotectina) i paràmetres serològics (proteïna C reactiva, fibrinogen), per determinar la seva possible utilitat com a marcadors predictius de recurrència després de la cirurgia resectiva.

Interfaz web para mostrar los genes según las relaciones que mantienen sus expresiones

La investigació entre les relacions dels nivells d’expressió dels gens aporta molta informació sobre els processos biològics i patològics. Mitjançant la tècnica de les microarrays es possibilita la investigació de les relacions d’expressió de milers de gens a la vegada. La finalitat d’aquest projecte es fent ús de l’aplicatiu web PCOPGene-Net, permetre la identificació dels gens per les relacions d’expressió no lineals que tenen amb la resta de gens i permetre també la identificació de les relacions d’expressió no lineals entre els gens d’una microarray.

Análisis bioinformáticos sobre la tecnología Hadoop

Desde el inicio del proyecto del genoma humano y su éxito en el año 2001 se han secuenciado genomas de multitud de especies. La mejora en las tecnologías de secuenciación ha generado volúmenes de datos con un crecimiento exponencial. El proyecto Análisis bioinformáticos sobre la tecnología Hadoop abarca la computación paralela de datos biológicos como son las secuencias de ADN. El estudio ha sido encauzado por la naturaleza del problema a resolver. El alineamiento de secuencias genéticas con el paradigma MapReduce.

Eficacia y Seguridad del tratamiento con Tocilizumab en pacientes con Artritis Reumatoide

L'artritis reumatoide (AR) és una malaltia inflamatòria crònica de caràcter sistèmic que afecta de manera preferent a les articulacions. El tractament de l'AR ha canviat de forma radical en l'última dècada. Això és a causa del desenvolupament de nous tractaments biològics dirigits contra molècules directament implicades en la patogènesi de l'AR. Un d'aquests tractaments és el Tocilizumab (RoACTEMRA ®) un anticòs monoclonal humanitzat que bloqueja l'acció de la Interleucina-6. TCZ ha estat aprovat recentment per al tractament de l'AR. El present projecte té com a objectiu avaluar la seguretat i eficàcia de TCZ en pacients amb AR inclosos en l'assaig clínic ACT-SURE (MA21573), provinents de la consulta externa monogràfica de pacients amb AR de l'Hospital Universitari Vall d'Hebron.

A comparative study of dyslipidaemia in men and woman with androgenic alopecia

Several studies have analyzed the relationship between androgenetic alopecia and cardiovascular disease (mainly heart disease). However few studies have analyzed lipid values in men and women separately. This case-control study included 300 patients consecutively admitted to an outpatient clinic, 150 with early onset androgenetic alopecia (80 males and 70 females) and 150 controls (80 males and 70 females) with other skin diseases. Female patients with androgenic alopecia showed significant higher triglycerides values (123.8 vs 89.43 mg/dl, p = 0.006), total cholesterol values (196.1 vs 182.3 mg/dl, p = 0.014), LDL-C values (114.1 vs 98.8 mg/dl, p = 0.0006) and lower HDL-C values (56.8 vs 67.7 mg/dl, p <0.0001) versus controls respectively. Men with androgenic alopecia showed significant higher triglycerides values (159.7 vs 128.7 mg/dl, p = 0.04) total cholesterol values (198.3 vs 181.4 mg/dl, p = 0.006) and LDL-C values (124.3 vs 106.2, p = 0.0013) versus non-alopecic men. A higher prevalence of dyslipidemia in women and men with androgenic alopecia has been found. The elevated lipid values in these patients may contribute, alongside other mechanisms, to the development of cardiovascular disease in patient with androgenic alopecia.

Clinical pharmacogenomic testing of KRAS, BRAF and EGFR mutations by high resolution melting analysis and ultra-deep pyrosequencing

BACKGROUND: Epidermal growth factor receptor (EGFR) and its downstream factors KRAS and BRAF are mutated in several types of cancer, affecting the clinical response to EGFR inhibitors. Mutations in the EGFR kinase domain predict sensitivity to the tyrosine kinase inhibitors gefitinib and erlotinib in lung adenocarcinoma, while activating point mutations in KRAS and BRAF confer resistance to the anti-EGFR monoclonal antibody cetuximab in colorectal cancer. The development of new generation methods for systematic mutation screening of these genes will allow more appropriate therapeutic choices. METHODS: We describe a high resolution melting (HRM) assay for mutation detection in EGFR exons 19-21, KRAS codon 12/13 and BRAF V600 using formalin-fixed paraffin-embedded samples. Somatic variation of KRAS exon 2 was also analysed by massively parallel pyrosequencing of amplicons with the GS Junior 454 platform. RESULTS: We tested 120 routine diagnostic specimens from patients with colorectal or lung cancer. Mutations in KRAS, BRAF and EGFR were observed in 41.9%, 13.0% and 11.1% of the overall samples, respectively, being mutually exclusive. For KRAS, six types of substitutions were detected (17 G12D, 9 G13D, 7 G12C, 2 G12A, 2 G12V, 2 G12S), while V600E accounted for all the BRAF activating mutations. Regarding EGFR, two cases showed exon 19 deletions (delE746-A750 and delE746-T751insA) and another two substitutions in exon 21 (one showed L858R with the resistance mutation T590M in exon 20, and the other had P848L mutation). Consistent with earlier reports, our results show that KRAS and BRAF mutation frequencies in colorectal cancer were 44.3% and 13.0%, respectively, while EGFR mutations were detected in 11.1% of the lung cancer specimens. Ultra-deep amplicon pyrosequencing successfully validated the HRM results and allowed detection and quantitation of KRAS somatic mutations. CONCLUSIONS: HRM is a rapid and sensitive method for moderate-throughput cost-effective screening of oncogene mutations in clinical samples. Rather than Sanger sequence validation, next-generation sequencing technology results in more accurate quantitative results in somatic variation and can be achieved at a higher throughput scale.

Oxidative stress is increased in critically ill patients according to antioxidant vitamins intake, independent of severity: a cohort study

Introduction. Critically ill patients suffer from oxidative stress caused by reactive oxygen species (ROS) and reactive nitrogen species (RNS). Although ROS/RNS are constantly produced under normal circumstances, critical illness can drastically increase their production. These patients have reduced plasma and intracellular levels of antioxidants and free electron scavengers or cofactors, and decreased activity of the enzymatic system involved in ROS detoxification. The pro-oxidant/antioxidant balance is of functional relevance during critical illness because it is involved in the pathogenesis of multiple organ failure. In this study the objective was to evaluate the relation between oxidative stress in critically ill patients and antioxidant vitamin intake and severity of illness. Methods. Spectrophotometry was used to measure in plasma the total antioxidant capacity and levels of lipid peroxide, carbonyl group, total protein, bilirubin and uric acid at two time points: at intensive care unit (ICU) admission and on day seven. Daily diet records were kept and compliance with recommended dietary allowance (RDA) of antioxidant vitamins (A, C and E) was assessed. Results. Between admission and day seven in the ICU, significant increases in lipid peroxide and carbonyl group were associated with decreased antioxidant capacity and greater deterioration in Sequential Organ Failure Assessment score. There was significantly greater worsening in oxidative stress parameters in patients who received antioxidant vitamins at below 66% of RDA than in those who received antioxidant vitamins at above 66% of RDA. An antioxidant vitamin intake from 66% to 100% of RDA reduced the risk for worsening oxidative stress by 94% (ods ratio 0.06, 95% confidence interval 0.010 to 0.39), regardless of change in severity of illness (Sequential Organ Failure Assessment score). Conclusion. The critical condition of patients admitted to the ICU is associated with worsening oxidative stress. Intake of antioxidant vitamins below 66% of RDA and alteration in endogenous levels of substances with antioxidant capacity are related to redox imbalance in critical ill patients. Therefore, intake of antioxidant vitamins should be carefully monitored so that it is as close as possible to RDA.

Prevención de los comportamientos sexuales de riesgo en los adolescentes: SIDA, otras enfermedades de transmisión sexual y embarazos no deseados

En la actualidad, los adolescentes son uno de los grupos que por sus características conductuales, cognitivas y sociales, se encuentran en mayor riesgo frente al posible contagio con el VIH. Esta amenaza para la salud y el bienestar de los adolescentes, se ha venido a sumar a otros problemas ya existentes en este colectivo: los embarazos no deseados y las enfermedades de transmisión sexual (ETS), que también se derivan de la no utilización de precauciones en las relaciones sexuales. En este trabajo se exponen diversos factores biológicos, psicológicos (conductuales y cognitivos) y sociales que pueden facilitar, dificultar o impedir los comportamientos sexuales de prevención de los adolescentes, y se revisan y valoran algunas de las intervenciones preventivas realizadas. A partir de esta revisión se argumenta sobre la conveniencia de unificar los programas para la prevención simultánea de los tres trastornos, maximizando de esta forma los recursos disponibles

Urinary aminopeptidase activities as early and predictive biomarkers of renal dysfunction in cisplatin-treated rats

This study analyzes the fluorimetric determination of alanyl- (Ala), glutamyl- (Glu), leucyl-cystinyl- (Cys) and aspartyl-aminopeptidase (AspAp) urinary enzymatic activities as early and predictive biomarkers of renal dysfunction in cisplatin-treated rats. Male Wistar rats (n = 8 each group) received a single subcutaneous injection of either saline or cisplatin 3.5 or 7 mg/kg, and urine samples were taken at 0, 1, 2, 3 and 14 days after treatment. In urine samples we determined Ala, Glu, Cys and AspAp activities, proteinuria, N-acetyl-β-D-glucosaminidase (NAG), albumin, and neutrophil gelatinase-associated lipocalin (NGAL). Plasma creatinine, creatinine clearance and renal morphological variables were measured at the end of the experiment. CysAp, NAG and albumin were increased 48 hours after treatment in the cisplatin 3.5 mg/kg treated group. At 24 hours, all urinary aminopeptidase activities and albuminuria were significantly increased in the cisplatin 7 mg/kg treated group. Aminopeptidase urinary activities correlated (p<0.011; r(2)>0.259) with plasma creatinine, creatinine clearance and/or kidney weight/body weight ratio at the end of the experiment and they could be considered as predictive biomarkers of renal injury severity. ROC-AUC analysis was made to study their sensitivity and specificity to distinguish between treated and untreated rats at day 1. All aminopeptidase activities showed an AUC>0.633. We conclude that Ala, Cys, Glu and AspAp enzymatic activities are early and predictive urinary biomarkers of the renal dysfunction induced by cisplatin. These determinations can be very useful in the prognostic and diagnostic of renal dysfunction in preclinical research and clinical practice.

A nutritional intervention study with hydrolyzed collagen in pre-pubertal Spanish children: influence on bone modeling biomarkers

Aim: The aim of the study was to investigate the influence of dietary intake of commercial hydrolyzed collagen (Gelatine Royal ®) on bone remodeling in pre-pubertal children. Methods: A randomized double-blind study was carried out in 60 children (9.42 ± 1.31 years) divided into three groups according to the amount of partially hydrolyzed collagen taken daily for 4 months: placebo (G-I, n = 18), collagen (G-II, n = 20) and collagen + calcium (G-III, n = 22) groups. Analyses of the following biochemical markers were carried out: total and bone alkaline phosphatase (tALP and bALP), osteocalcin, tartrate-resistant acid phosphatase (TRAP), type I collagen carboxy terminal telopeptide, lipids, calcium, 25-hydroxyvitamin D, insulin-like growth factor 1 (IGF-1), thyroid-stimulating hormone, free thyroxin and intact parathormone. Results: There was a significantly greater increase in serum IGF-1 in G-III than in G II (p < 0.01) or G-I (p < 0.05) during the study period, and a significantly greater increase in plasma tALP in G-III than in G-I (p < 0.05). Serum bALP behavior significantly (p < 0.05) differed between G-II (increase) and G-I (decrease). Plasma TRAP behavior significantly differed between G-II and G-I (p < 0.01) and between G-III and G-II (p < 0.05). Conclusion: Daily dietary intake of hydrolyzed collagen seems to have a potential role in enhancing bone remodeling at key stages of growth and development.

Bovine tuberculosis in Doñana Biosphere Reserve: the role of wild ungulates as disease reservoirs in the last Iberian lynx strongholds.

Doñana National Park (DNP) in southern Spain is a UNESCO Biosphere Reserve where commercial hunting and wildlife artificial feeding do not take place and traditional cattle husbandry still exists. Herein, we hypothesized that Mycobacterium bovis infection prevalence in wild ungulates will depend on host ecology and that variation in prevalence will reflect variation in the interaction between hosts and environmental risk factors. Cattle bTB reactor rates increased in DNP despite compulsory testing and culling of infected animals. In this study, 124 European wild boar, 95 red deer, and 97 fallow deer were sampled from April 2006 to April 2007 and analyzed for M. bovis infection. Modelling and GIS were used to identify risk factors and intra and inter-species relationships. Infection with M. bovis was confirmed in 65 (52.4%) wild boar, 26 (27.4%) red deer and 18 (18.5%) fallow deer. In the absence of cattle, wild boar M. bovis prevalence reached 92.3% in the northern third of DNP. Wild boar showed more than twice prevalence than that in deer (p<0.001). Modelling revealed that M. bovis prevalence decreased from North to South in wild boar (p<0.001) and red deer (p<0.01), whereas no spatial pattern was evidenced for fallow deer. Infection risk in wild boar was dependent on wild boar M. bovis prevalence in the buffer area containing interacting individuals (p<0.01). The prevalence recorded in this study is among the highest reported in wildlife. Remarkably, this high prevalence occurs in the absence of wildlife artificial feeding, suggesting that a feeding ban alone would have a limited effect on wildlife M. bovis prevalence. In DNP, M. bovis transmission may occur predominantly at the intra-species level due to ecological, behavioural and epidemiological factors. The results of this study allow inferring conclusions on epidemiological bTB risk factors in Mediterranean habitats that are not managed for hunting purposes. Our results support the need to consider wildlife species for the control of bTB in cattle and strongly suggest that bTB may affect animal welfare and conservation.

Different profiles of immune reconstitution in children and adults with HIV-infection after highly active antiretroviral therapy.

BACKGROUND Recent advances in characterizing the immune recovery of HIV-1-infected people have highlighted the importance of the thymus for peripheral T-cell diversity and function. The aim of this study was to investigate differences in immune reconstitution profiles after highly active antiretroviral therapy (HAART) between HIV-children and adults. METHODS HIV patients were grouped according to their previous clinical and immunological status: 9 HIV-Reconstituting-adults (HIV-Rec-adults) and 10 HIV-Reconstituting-children (HIV-Rec-children) on HAART with viral load (VL) or=500 cells/microL at least during 6 months before the study and CD4+