Discovering study-specific gene regulatory networks

This article has been made available through the Brunel Open Access Publishing Fund.Microarrays are commonly used in biology because of their ability to simultaneously measure thousands of genes under different conditions. Due to their structure, typically containing a high amount of variables but far fewer samples, scalable network analysis techniques are often employed. In particular, consensus approaches have been recently used that combine multiple microarray studies in order to find networks that are more robust. The purpose of this paper, however, is to combine multiple microarray studies to automatically identify subnetworks that are distinctive to specific experimental conditions rather than common to them all. To better understand key regulatory mechanisms and how they change under different conditions, we derive unique networks from multiple independent networks built using glasso which goes beyond standard correlations. This involves calculating cluster prediction accuracies to detect the most predictive genes for a specific set of conditions. We differentiate between accuracies calculated using cross-validation within a selected cluster of studies (the intra prediction accuracy) and those calculated on a set of independent studies belonging to different study clusters (inter prediction accuracy). Finally, we compare our method's results to related state-of-the art techniques. We explore how the proposed pipeline performs on both synthetic data and real data (wheat and Fusarium). Our results show that subnetworks can be identified reliably that are specific to subsets of studies and that these networks reflect key mechanisms that are fundamental to the experimental conditions in each of those subsets

Pacientes españoles con síndrome de hipoventilación central incluidos en el Registro europeo. Datos del 2015

Introducción El síndrome de hipoventilación central congénita (SHCC) es una enfermedad genética muy rara causada por mutaciones en PHOX2B; en 2010 se creó el Consorcio Europeo del Síndrome de Hipoventilación Central, que en 2012 implantó un Registro online de pacientes para optimizar su cuidado. Objetivo Conocer las características y la evolución de los pacientes españoles con SHCC y detectar áreas de mejora. Materiales y método Se analizaron los datos actualizados en diciembre del 2015 de los pacientes españoles del Registro europeo. Resultados Se registró a 38 pacientes, nacidos entre 1987 y 2013, procedentes de 18 hospitales. El 34, 2% eran mayores de 18 años. Han fallecido 3 pacientes. Aportaban estudio del gen PHOX2B 37 (97, 3%), 32 (86, 5%) con mutación. Los genotipos 20/25, 20/26 y 20/27 representaron el 84, 3% de las mutaciones. Las disautonomías fueron más frecuentes y graves en portadores de genotipos con mayores expansiones de polialaninas. El 47% de pacientes asociaba alteraciones oculares, el 16% Hirschsprung, el 13% hipoglucemias y el 5% tumores. Treinta pacientes (79%) debutaron en el periodo neonatal y 8 (21%) posteriormente (inicio/diagnóstico tardío). Ocho niños (21%) recibieron inicialmente ventilación domiciliaria con mascarilla; 5 eran lactantes con comienzo neonatal, 2 de ellos precisaron cambio a traqueostomía tras presentar parada cardiorrespiratoria; ambos tenían mutaciones graves. Han sido decanulados y transferidos a mascarilla el 34, 3% de los pacientes (edad media: 13, 7 años). El 29, 4% de los niños escolarizados precisaron refuerzo educativo. Conclusión La implementación del Registro en España de pacientes con SHCC ha permitido identificar aspectos relevantes para optimizar sus cuidados, tales como la importancia del estudio genético para el diagnóstico y la estimación de gravedad, la frecuencia elevada de alteraciones oculares y de necesidad de refuerzo educativo, y algunas limitaciones de las técnicas ventilatorias. Introduction Congenital Central Hypoventilation Syndrome (CCHS) is a very rare genetic disease. In 2012 the European Central Hypoventilation Syndrome (EuCHS) Consortium created an online patient registry in order to improve care. Aim To determine the characteristics and outcomes of Spanish patients with CCHS, and detect clinical areas for improvement. Materials and method An assessment was made on the data from Spanish patients in the European Registry, updated on December 2015. Results The Registry contained 38 patients, born between 1987 and 2013, in 18 hospitals. Thirteen (34.2%) were older than 18 years. Three patients had died. Genetic analysis identified PHOX2B mutations in 32 (86.5%) out of 37 patients assessed. The 20/25, 20/26 and 20/27 polyalanine repeat mutations (PARMs) represented 84.3% of all mutations. Longer PARMs had more, as well as more severe, autonomic dysfunctions. Eye diseases were present in 47%, with 16% having Hirschsprung disease, 13% with hypoglycaemia, and 5% with tumours. Thirty patients (79%) required ventilation from the neonatal period onwards, and 8 (21%) later on in life (late onset/presentation). Eight children (21%) were using mask ventilation at the first home discharge. Five of them were infants with neonatal onset, two of them, both having a severe mutation, were switched to tracheostomy after cardiorespiratory arrest at home. Approximately one-third (34.3%) of patients were de-cannulated and switched to mask ventilation at a mean age of 13.7 years. Educational reinforcement was required in 29.4% of children attending school. Conclusion The implementation of the EuCHS Registry in Spain has identified some relevant issues for optimising healthcare, such as the importance of genetic study for diagnosis and assessment of severity, the high frequency of eye disease and educational reinforcement, as well as some limitations in ventilatory techniques

A922 Sequential measurement of 1 hour creatinine clearance (1-CRCL) in critically ill patients at risk of acute kidney injury (AKI)

Meeting abstrac

Biochemical characterization of stage-specific isoforms of aspartate aminotransferases from Trypanosoma cruzi and Trypanosoma brucei.

Three genes encoding putative aspartate aminotransferases (ASATs) were identified in the Trypanosoma cruzi genome. Two of these ASAT genes, presumably corresponding to a cytosolic and mitochondrial isoform, were cloned and expressed as soluble His-tagged proteins in Escherichia coli. The specific activities determined for both T. cruzi isozymes were notably higher than the values previously reported for Trypanosoma brucei orthologues. To confirm these differences, T. brucei mASAT and cASAT were also expressed as His-tagged enzymes. The kinetic analysis showed that the catalytic parameters of the new recombinant T. brucei ASATs were very similar to those determined for T. cruzi orthologues. The cASATs from both parasites displayed equally broad substrate specificities, while mASATs were highly specific towards aspartate/2-oxoglutarate. The subcellular localization of the mASAT was confirmed by digitonin extraction of intact epimastigotes. At the protein level, cASAT is constitutively expressed in T. brucei, whereas mASAT is down-regulated in the bloodstream forms. By contrast in T. cruzi, mASAT is expressed along the whole life cycle, whereas cASAT is specifically induced in the mammalian stages. Similarly, the expression of malate dehydrogenases (MDHs) is developmentally regulated in T. cruzi: while glycosomal MDH is only expressed in epimastigotes and mitochondrial MDH is present in the insect and mammalian stages. Taken together, these findings provide evidence for a metabolically active mitochondrion in the mammalian stages of T. cruzi, and suggest that the succinate excreted by amastigotes more likely represents a side product of an at least partially operative Krebs cycle, than an end product of glycosomal catabolism

Environmental conditions for akaganeite formation in marine atmosphere mild steel corrosion products and its characterization

© 2015, NACE International. The corrosion of mild steel in chloride-rich atmospheres is a highly topical issue. The formation of the oxyhydroxide akaganeite (β-FeOOH) in this type of atmosphere leads to a notable acceleration of the steel corrosion process. The scientific literature contains many references to outdoor marine atmospheric tests, but so far has failed to clarify two basic matters in relation to akaganeite: the environmental conditions necessary for its formation, and its morphological characterization. Research has been performed at three atmospheric corrosion stations located at Cabo Vilano wind farm (Camariñas, Spain) at different distances from the shoreline (332, 590, and 2,400 m), with chloride deposition rates of 390, 74, and 29 mg/m2/day, respectively, with the exposure of mild steel specimens for 1 year. This paper reports the environmental conditions that generally led to the formation of akaganeite: an annual average relative humidity of around 80% or higher, and simultaneously, an annual average chloride deposition rate of approximately 60 mg/m2/day or higher. Rigorous characterization of akaganeite was performed by x-ray diffraction, scanning electron microscopy/energy dispersive spectroscopy, and transmission electron microscopy/selected area electron diffraction.The authors gratefully acknowledge the financial support for this study from the Ministry of Science and Innovation of Spain (CICYT-MAT 2008-06649). The authors would like to express their gratitude to the companies ENEL and GAS NATURAL for the facilities provided and for allowing the location of the corrosion stations at Cabo Vilano wind farm (Camariñas, Spain). They would also like to thank the Spanish Meteorology Agency for the data provided on meteorological parameters in the study area. I. Díaz also acknowledges the Ph.D. scholarship financed by CSIC JAE Programme.Peer Reviewe

Genome Wide Association Study for Drought, Aflatoxin Resistance, and Important Agronomic Traits of Maize Hybrids in the Sub-Tropics

<div><p>The primary maize (<i>Zea mays</i> L.) production areas are in temperate regions throughout the world and this is where most maize breeding is focused. Important but lower yielding maize growing regions such as the sub-tropics experience unique challenges, the greatest of which are drought stress and aflatoxin contamination. Here we used a diversity panel consisting of 346 maize inbred lines originating in temperate, sub-tropical and tropical areas testcrossed to stiff-stalk line Tx714 to investigate these traits. Testcross hybrids were evaluated under irrigated and non-irrigated trials for yield, plant height, ear height, days to anthesis, days to silking and other agronomic traits. Irrigated trials were also inoculated with <i>Aspergillus flavus</i> and evaluated for aflatoxin content. Diverse maize testcrosses out-yielded commercial checks in most trials, which indicated the potential for genetic diversity to improve sub-tropical breeding programs. To identify genomic regions associated with yield, aflatoxin resistance and other important agronomic traits, a genome wide association analysis was performed. Using 60,000 SNPs, this study found 10 quantitative trait variants for grain yield, plant and ear height, and flowering time after stringent multiple test corrections, and after fitting different models. Three of these variants explained 5–10% of the variation in grain yield under both water conditions. Multiple identified SNPs co-localized with previously reported QTL, which narrows the possible location of causal polymorphisms. Novel significant SNPs were also identified. This study demonstrated the potential to use genome wide association studies to identify major variants of quantitative and complex traits such as yield under drought that are still segregating between elite inbred lines.</p></div