Structural-Based Modeling in Protein Engineering. A Must Do

Biotechnological solutions will be a key aspect in our immediate future society, where optimized enzymatic processes through enzyme engineering might be an important solution for waste transformation, clean energy production, biodegradable materials, and green chemistry, for example. Here we advocate the importance of structural-based bioinformatics and molecular modeling tools in such developments. We summarize our recent experiences indicating a great prediction/success ratio, and we suggest that an early in silico phase should be performed in enzyme engineering studies. Moreover, we demonstrate the potential of a new technique combining Rosetta and PELE, which could provide a faster and more automated procedure, an essential aspect for a broader use.This work has also been supported by predoctoral fellowships FPU19/00608 and PRE2020-091825, and the PID2019-106370RBI00/AEI/10.13039/501100011033 grant from the Spanish Ministry of Science and Innovation.Peer ReviewedPostprint (author's final draft

EP-Pred: A machine learning tool for bioprospecting promiscuous ester hydrolases

When bioprospecting for novel industrial enzymes, substrate promiscuity is a desirable property that increases the reusability of the enzyme. Among industrial enzymes, ester hydrolases have great relevance for which the demand has not ceased to increase. However, the search for new substrate promiscuous ester hydrolases is not trivial since the mechanism behind this property is greatly influenced by the active site’s structural and physicochemical characteristics. These characteristics must be computed from the 3D structure, which is rarely available and expensive to measure, hence the need for a method that can predict promiscuity from sequence alone. Here we report such a method called EP-pred, an ensemble binary classifier, that combines three machine learning algorithms: SVM, KNN, and a Linear model. EP-pred has been evaluated against the Lipase Engineering Database together with a hidden Markov approach leading to a final set of ten sequences predicted to encode promiscuous esterases. Experimental results confirmed the validity of our method since all ten proteins were found to exhibit a broad substrate ambiguity.This study was conducted under the auspices of the FuturEnzyme and Oxipro Projects funded by the European Union’s Horizon 2020 Research and Innovation Programme under Grant Agreement No. 101000327 and 101000607. We also acknowledge financial support under Grants PID2020-112758RB-I00 (M.F.), PID2019-106370RB-I00 (V.G.) and PDC2021-121534-I00 (M.F.) and PID2019-106370RB-I00/AEI/10.13039/501100011033 (A.R.-M.), from the Ministerio de Ciencia e Innovación, Agencia Estatal de Investigación (AEI) (Digital Object Identifier 10.13039/501100011033), Fondo Europeo de Desarrollo Regional (FEDER) and the European Union (“NextGen-erationEU/PRTR”), and Grant 2020AEP061 (M.F.) from the Agencia Estatal CSIC.Peer ReviewedPostprint (published version

La administración de operaciones en Sociedad Anónima Industrias Celulosa Aragonesa (SAICA)

Saica es en la actualidad una empresa líder en el sector papelero mundial, dedicada a la producción en grandes cantidades de papel para cartón ondulado. Además, también posee varios centros propios de recuperación de papel y cartón, lo que hace que sea muy respetuosa con el medio ambiente y la sociedad en general. Hasta llegar a convertirse en una gran empresa de este sector, Saica tuvo que dedicar innumerables esfuerzos en innovación, ya que el papel es un producto que se encuentra en una etapa de madurez del ciclo de vida del producto/s, al cual tenemos que mantener activo en todo momento mediante continuas innovaciones. Por ello, en el presente trabajo se considera adecuado centrarse en dos aspectos fundamentales como son la innovación y el medio ambiente. Estos dos temas son importantes en la actualidad de todas las empresas independientemente del sector en el que operen, más concretamente el papelero. El objetivo del presente trabajo es el estudio del sistema de producción de papel y cartón efectuado por Saica, considerando la innovación y medio ambiente por su importancia para la empresa. Ello se considera fundamental para comprender posibles fallos y seguir innovando, no solo mediante la implantación de nuevas tecnologías que puedan surgir en los mercados, sino proponiendo actuaciones efectivas y eficaces en el mundo. De manera que se trabaje adecuadamente con la sociedad y el medio ambiente deseable para las generaciones futuras, siendo un pilar fundamental para crear valor en la sociedad y obtener una ventaja competitiva frente a los competidores

Linfomas B Agresivos: Serie de Casos y Revisión Clínico-Terapéutica

Fondo: Desde 1997, el protocolo R-CHOP (ciclofosfamida, doxorrubicina, vincristina, prednisona y rituximab) se ha mantenido como tratamiento estándar del linfoma B difuso de células grandes (DLBCL). Sin embargo, estudios posteriores desarrollaron el protocolo R-EPOCH (ciclofosfamida, doxorrubicina, etopósido, vincristina, prednisona y rituximab), caracterizado por ser un protocolo dinámico, basado en la terapia infusional prolongada y un sistema de escalada de dosis, con resultados prometedores, especialmente, en pacientes de alto riesgo. Se propone la evaluación de la respuesta a R-EPOCH mediante un estudio descriptivo retrospectivo de una serie casos de linfomas B de alto riesgo. Además de una revisión clínico-terapéutica breve del DLBCL. Método: La serie incluyó 29 casos tratados con R-EPOCH, mayoritariamente DLBCL, no tratados previamente, con una mediana de edad de 48 años (rango 16 a 76 años), y factores de mal pronóstico: estadio ≥ III (86,2%), masa bulky > 7,5 cm (44,83%) e IPI de alto/alto-intermedio (71,43%). También se valoraron la expresión de biomarcadores e índice de proliferación. Resultados: La media de tiempo de seguimiento fue de 5,39 años, la supervivencia global se mantuvo en 79,40% a los 6 años, mientras la supervivencia libre de eventos se mantuvo en 78,78% a los 2 años. Las remisiones completas fueron de 89,65%, con un porcentaje de recaída del 11,54%. En algunos casos se incluyó tratamiento quimioterápico, radioterapia y TASPE complementarios a R-EPOCH. El total de defunciones supuso el 17,24%, siendo en su totalidad pacientes que recayeron o no alcanzaron remisión completa tras tratamiento de 1º línea. En ningún caso se mostraron eventos tóxicos de gravedad. Conclusiones: Al igual que estudios previos, nuestros datos han demostrado una buena eficacia del protocolo R-EPOCH en linfomas B de alto riesgo, manteniendo una toxicidad tolerable. Por lo tanto, R-EPOCH podría ser una buena alternativa en este grupo de pacientes. Sin embargo, serán necesarios ensayos clínicos randomizados de gran tamaño para comparar la eficacia entre R-CHOP y R-EPOCH. La mortalidad en enfermedad refractaria o recaída es elevada, lo que muestra una escasa eficacia de los tratamientos de segunda línea. La expresión de biomarcadores y el índice de proliferación elevado no se asociaron a peor pronóstico.<br /

Switching the substrate preference of fungal aryl-alcohol oxidase: towards stereoselective oxidation of secondary benzyl alcohols

Oxidation of primary alcohols by aryl-alcohol oxidase (AAO), a flavoenzyme that provides H2O2 to fungal peroxidases for lignin degradation in nature, is achieved by concerted hydroxyl proton transfer and stereoselective hydride abstraction from the pro-R benzylic position. In racemic secondary alcohols, the R-hydrogen abstraction would result in the selective oxidation of the S-enantiomer to the corresponding ketone. This stereoselectivity of AAO may be exploited for enzymatic deracemization of chiral mixtures and isolation of R-enantiomers of industrial interest by switching the enzyme activity from primary to secondary alcohols. A combination of computational simulations and mutagenesis has been used to produce AAO variants with increased activity on secondary alcohols, using the already available F501A variant of Pleurotus eryngii AAO as a starting point. Adaptive-PELE simulations for the diffusion of (S)-1-(p-methoxyphenyl)-ethanol in this variant allowed Ile500 to be identified as one of the key residues with a higher number of contacts with the substrate during its transition from the solvent to the active site. Substitution of Ile500 produced more efficient variants for the oxidation of several secondary alcohols, and the I500M/F501W double variant was able to fully oxidize (after 75 min) with high selectivity (ee >99%) the S-enantiomer of the model secondary aryl-alcohol (±)-1-(p-methoxyphenyl)-ethanol, while the R-enantiomer remained unreacted.This work was supported by the INDOX (KBBE-2013-7-613549) EU project and by the BIO2017-86559-R (GenoBioref), CTQ2016-79138-R and BIO2016-79106-R projects of the Spanish Ministry of Economy, Industry and Competitiveness, cofinanced by FEDER funds. Pedro Merino (University of Zaragoza, Spain) is acknowledged for his suggestions on chiral HPLC analyses.Peer ReviewedAward-winningPostprint (published version

Sub-micro- and nano-sized polyethylene terephthalate deconstruction with engineered protein nanopores

The identification or design of biocatalysts to mitigate the accumulation of plastics, including sub-micro- and nano-sized polyethylene terephthalate (nPET), is becoming a global challenge. Here we computationally incorporated two hydrolytic active sites with geometries similar to that of Idionella sakaiensis PET hydrolase, to fragaceatoxin C (FraC), a membrane pore-forming protein. FraCm1/m2 could be assembled into octameric nanopores (7.0 nm high × 1.6–6.0 nm entry), which deconstructed (40 °C, pH 7.0) nPET from GoodFellow, commodities and plastic bottles. FraCm1 and FraCm2 degrade nPET by endo- and exo-type chain scission. While FraCm1 produces bis(2-hydroxyethyl) terephthalate as the main product, FraCm2 yields a high diversity of oligomers and terephthalic acid. Mechanistic and biochemical differences with benchmark PET hydrolases, along with pore and nPET dynamics, suggest that these pore-forming protein catalytic nanoreactors do not deconstruct macro-PET but are promising in nanotechnology for filtering, capturing and breaking down nPET, for example, in wastewater treatment plants.This study was conducted under the auspices of the FuturEnzyme Project funded by the European Union’s Horizon 2020 Research and Innovation Programme under the auspices of the FuturEnzyme Project (grant agreement no. 101000327) and the PlasticsFatE project (grant agreement no. 95921), and Horizon Europe Research and Innovation Programme under grant agreement no. GA101060625 (Nymphe project). We also acknowledge financial support under grants PID2020-112758RB-I00 (M.F.), PDC2021-121534-I00 (M.F.), TED2021-130544B-I00 (M.F.), PID2019-106370RB-I00 (V.G.) and PID2019-105838RB-C31 (F.J.P.) from the Ministerio de Ciencia e Innovación, Agencia Estatal de Investigación (AEI) (Digital Object Identifier MCIN/AEI/10.13039/501100011033), Fondo Europeo de Desarrollo Regional (ERDF) A way of making Europe and the European Union NextGenerationEU/PRTR, UCM-Banco Santander Grants PR87/19-22556 and PR108/20-26896 and UnaEuropa (Unano) SF2106 (to A.M.P.). S.G.-L. was supported by a Real Colegio Complutense Postdoctoral Fellowship for Distinguished Junior Scholars. S.R. thanks the Spanish Ministry of Science and Innovation for a PhD fellowship (FPU19/00608). D.H.-M. thanks Complutense University of Madrid and Banco Santander for a PhD fellowship (CT82/20/CT83/20). A.R.-M. thanks the Spanish Ministry of Science and Innovation for a PhD fellowship (PRE2020-091825) and the project PID2019-106370RB-I00. We thank M. J. Vicente for the ESI–MS analysis, performed at the Servicio Interdepartamental de Investigación (SIDI) from the Autonomous University of Madrid, Spain.Peer Reviewed"Article signat per 16 autors/es: Ana Robles-Martín, Rafael Amigot-Sánchez, Laura Fernandez-Lopez, Jose L. Gonzalez-Alfonso, Sergi Roda, Víctor Alcolea-Rodriguez, Diego Heras-Márquez, David Almendral, Cristina Coscolín, Francisco J. Plou, Raquel Portela, Miguel A. Bañares, Álvaro Martínez-del-Pozo, Sara García-Linares, Manuel Ferrer & Víctor Guallar"Postprint (published version

Serum selenium concentrations and diabetes in U.S. adults : National Health and Nutrition Examination Survey (NHANES) 2003–2004

Background: Increasing evidence suggests that high selenium levels are associated with diabetes and other cardiometabolic risk factors. Objectives: We evaluated the association of serum selenium concentrations with fasting plasma glucose, glycosylated hemoglobin levels, and diabetes in the most recently available representative sample of the U.S. population. Methods: We used a cross-sectional analysis of 917 adults ≥ 40 years of age who had a fasting morning blood sample in the National Health and Nutrition Examination Survey 2003–2004. We evaluated the association of serum selenium, measured by inductively coupled plasma-dynamic reaction cell-mass spectrometry, and diabetes, defined as a self-report of current use of hypoglycemic agents or insulin or as fasting plasma glucose ≥ 126 mg/dL. Results: Mean serum selenium was 137.1 μg/L. The multivariable adjusted odds ratio [95% confidence interval (CI)] for diabetes comparing the highest quartile of serum selenium (≥ 147 μg/L) with the lowest (< 124 μg/L) was 7.64 (3.34–17.46). The corresponding average differences (95% CI) in fasting plasma glucose and glycosylated hemoglobin were 9.5 mg/dL (3.4–15.6 mg/dL) and 0.30% (0.14–0.46%), respectively. In spline regression models, the prevalence of diabetes as well as glucose and glycosylated hemoglobin levels increased with increasing selenium concentrations up to 160 μg/L. Conclusions: In U.S. adults, high serum selenium concentrations were associated with higher prevalence of diabetes and higher fasting plasma glucose and glycosylated hemoglobin levels. Given high selenium intake in the U.S. population, further research is needed to determine the role of excess selenium levels in the development or the progression of diabetes

Combined healthy behaviors and healthcare services use in older adults

Data on the combined impact of healthy behaviors on healthcare use in older adults are limited. Methods Study with community-dwelling individuals aged ≥60 years from the Spanish Seniors-ENRICA cohort, recruited in 2008–2010, followed through 2012–2013, and analyzed in 2016 (N=2,021). At baseline, the following healthy behaviors were self-reported: three traditional (never smoking, being physically active, having a healthy diet) and three emerging (sleeping 7–8 hours/day, sitting &lt; 8 hours/day, not living alone). Outcomes were self-reported polypharmacy (five or more drugs per day), primary care physician visits (one or more per month), medical specialist visits (more than one per year), and hospitalization (one or more in the last year). The associations between baseline healthy behaviors and healthcare services used in 2012–2013 were summarized with ORs and 95% CIs from multiple logistic regression, adjusting for demographics, lifestyles, comorbidities, and baseline health services used. Results Most single healthy behaviors were associated with lower use of most health services. Compared with participants with zero or one healthy behavior, those with five or six healthy behaviors showed lower risk of polypharmacy (OR=0.46, 95% CI=0.24, 0.85, p-trend=0.001), visits to the primary care physician (OR=0.50, 95% CI=0.26, 0.96, p-trend=0.013), and hospitalization (OR=0.50, 95% CI=0.24, 1.01, p-trend=0.016). No association was found with visits to the medical specialist. Conclusions The combination of five to six healthy behaviors in older adults is associated with half the risk of polypharmacy and using several healthcare services. In an era of constrained resources in most countries, this information may help inform health policy to control healthcare spending in the futureSpecific funding for this study was obtained from Fondo de Investigación Sanitaria (FIS) grant PI13/02321 and PI16/ 01460 (Instituto de Salud Carlos III and FEDER/FSE). RFP-T was supported by the National Government of Ecuador through the National Institution of Higher Education, Science, Technology and Innovation (SENESCYT

Arsenic Exposure and Hypertension: A Systematic Review

Background: Environmental exposure to arsenic has been linked to hypertension in persons living in arsenic-endemic areas