MOMIC: A multi-omics pipeline for data analysis, integration and interpretation

Background and Objectives: The burst of high-throughput omics technologies has given rise to a new era in systems biology, offering an unprecedented scenario for deriving meaningful biological knowledge through the integration of different layers of information. Methods: We have developed a new software tool, MOMIC, that guides the user through the application of different analysis on a wide range of omic data, from the independent single-omics analysis to the combination of heterogeneous data at different molecular levels. Results: The proposed pipeline is developed as a collection of Jupyter notebooks, easily editable, reproducible and well documented. It can be modified to accommodate new analysis workflows and data types. It is accessible via momic.us.es, and as a docker project available at github that can be locally installed. Conclusions: MOMIC offers a complete analysis environment for analysing and integrating multi-omics data in a single, easy-to-use platform.Ministerio de Economía y Competitividad TIN2017-88209-C2-2-RJunta de Andalucía P18-RT-2778Junta de Andalucía US-1263341Ministerio de Ciencia e Innovación IPT-2011-0952-90000

Application of crosslinked polybenzimidazole-poly(Vinyl benzyl chloride) anion exchange membranes in direct ethanol fuel cells

Crosslinked membranes have been synthesized by a casting process using polybenzimidazole (PBI) and poly(vinyl benzyl chloride) (PVBC). The membranes were quaternized with 1,4-diazabicyclo[2.2.2]octane (DABCO) to obtain fixed positive quaternary ammonium groups. XPS analysis has showed insights into the changes from crosslinked to quaternized membranes, demonstrating that the crosslinking reaction and the incorporation of DABCO have occurred, while the13C-NMR corroborates the reaction of DABCO with PVBC only by one nitrogen atom. Mechanical properties were evaluated, obtaining maximum stress values around 72 MPa and 40 MPa for crosslinked and quaternized membranes, respectively. Resistance to oxidative media was also satisfactory and the membranes were evaluated in single direct ethanol fuel cell. PBI-c-PVBC/OH 1:2 membrane obtained 66 mW cm−2 peak power density, 25% higher than commercial PBI membranes, using 0.5 bar backpressure of pure O2 in the cathode and 1 mL min−1 KOH 2M EtOH 2 M aqueous solution in the anode. When the pressure was increased, the best performance was obtained by the same membrane, reaching 70 mW cm−2 peak power density at 2 bar O2 backpressure. Based on the characterization and single cell performance, PBI-c-PVBC/OH membranes are considered promising candidates as anion exchange electrolytes for direct ethanol fuel cells.Fil: Herranz, Daniel. Universidad Autónoma de Madrid; EspañaFil: Coppola, Roxana Elisabeth. Instituto Nacional de Tecnología Industrial; ArgentinaFil: Escudero Cid, Ricardo. Universidad Autónoma de Madrid; EspañaFil: Ochoa Romero, Kerly. Universidad Autónoma de Madrid; EspañaFil: D'accorso, Norma Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Centro de Investigaciones en Hidratos de Carbono. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Centro de Investigaciones en Hidratos de Carbono; ArgentinaFil: Pérez Flores, Juan Carlos. Universidad de Castilla-La Mancha; EspañaFil: Canales Vázquez, Jesús. Universidad de Castilla-La Mancha; EspañaFil: Palacio, Carlos. Universidad Autónoma de Madrid; EspañaFil: Abuin, Graciela Carmen. Instituto Nacional de Tecnología Industrial; ArgentinaFil: Ocón, Pilar. Universidad Autónoma de Madrid; Españ

Molecular method for the characterization of Coxiella burnetii from clinical and environmental samples: variability of genotypes in Spain

BACKGROUND: Coxiella burnetii is a highly clonal microorganism which is difficult to culture, requiring BSL3 conditions for its propagation. This leads to a scarce availability of isolates worldwide. On the other hand, published methods of characterization have delineated up to 8 different genomic groups and 36 genotypes. However, all these methodologies, with the exception of one that exhibited limited discriminatory power (3 genotypes), rely on performing between 10 and 20 PCR amplifications or sequencing long fragments of DNA, which make their direct application to clinical samples impracticable and leads to a scarce accessibility of data on the circulation of C. burnetii genotypes. RESULTS: To assess the variability of this organism in Spain, we have developed a novel method that consists of a multiplex (8 targets) PCR and hybridization with specific probes that reproduce the previous classification of this organism into 8 genomic groups, and up to 16 genotypes. It allows for a direct characterization from clinical and environmental samples in a single run, which will help in the study of the different genotypes circulating in wild and domestic cycles as well as from sporadic human cases and outbreaks. The method has been validated with reference isolates. A high variability of C. burnetii has been found in Spain among 90 samples tested, detecting 10 different genotypes, being those adaA negative associated with acute Q fever cases presenting as fever of intermediate duration with liver involvement and with chronic cases. Genotypes infecting humans are also found in sheep, goats, rats, wild boar and ticks, and the only genotype found in cattle has never been found among our clinical samples. CONCLUSIONS: This newly developed methodology has permitted to demonstrate that C. burnetii is highly variable in Spain. With the data presented here, cattle seem not to participate in the transmission of C. burnetii to humans in the samples studied, while sheep, goats, wild boar, rats and ticks share genotypes with the human population

NKG2D-CAR memory T cells target pediatric T-cell acute lymphoblastic leukemia in vitro and in vivo but fail to eliminate leukemia initiating cells

Introduction Refractory/relapsed pediatric acute leukemia are still clinically challenging and new therapeutic strategies are needed. Interactions between Natural Killer Group 2D (NKG2D) receptor, expressed in cytotoxic immune cells, and its ligands (NKG2DL), which are upregulated in leukemic blasts, are important for anti-leukemia immunosurveillance. Nevertheless, leukemia cells may develop immunoescape strategies as NKG2DL shedding and/or downregulation. Methods In this report, we analyzed the anti-leukemia activity of NKG2D chimeric antigen receptor (CAR) redirected memory (CD45RA ⁻ ) T cells in vitro and in a murine model of T-cell acute lymphoblastic leukemia (T-ALL). We also explored in vitro how soluble NKG2DL (sNKG2DL) affected NKG2D-CAR T cells’ cytotoxicity and the impact of NKG2D-CAR T cells on Jurkat cells gene expression and in vivo functionality. Results In vitro , we found NKG2D-CAR T cells targeted leukemia cells and showed resistance to the immunosuppressive effects exerted by sNKG2DL. In vivo , NKG2D-CAR T cells controlled T cell leukemia burden and increased survival of the treated mice but failed to cure the animals. After CAR T cell treatment, Jurkat cells upregulated genes related to proliferation, survival and stemness, and in vivo , they exhibited functional properties of leukemia initiating cells. Discussion The data here presented suggest, that, in combination with other therapeutic approaches, NKG2D-CAR T cells could be a novel treatment for pediatric T-ALL

Optimizing the procedure to manufacture clinical‐grade NK cells for adoptive immunotherapy

Natural killer (NK) cells represent promising tools for cancer immunotherapy. We report the optimization of an NK cell activation–expansion process and its validation on clinical‐scale. Methods: RPMI‐1640, stem cell growth medium (SCGM), NK MACS and TexMACS were used as culture mediums. Activated and expanded NK cells (NKAE) were obtained by coculturing total peripheral blood mononuclear cells (PBMC) or CD45RA+ cells with irradiated K562mbIL15‐41BBL or K562mbIL21‐41BBL. Fold increase, NK cell purity, activation status, cytotoxicity and transcriptome profile were analyzed. Clinical‐grade NKAE cells were manufactured in CliniMACS Prodigy. Results: NK MACS and TexMACs achieved the highest NK cell purity and lowest T cell contamination. Obtaining NKAE cells from CD45RA+ cells was feasible although PBMC yielded higher total cell numbers and NK cell purity than CD45RA+ cells. The highest fold expansion and NK purity were achieved by using PBMC and K562mbIL21‐41BBL cells. However, no differences in activation and cytotoxicity were found when using either NK cell source or activating cell line. Transcriptome profile showed to be different between basal NK cells and NKAE cells expanded with K562mbIL21‐41BBL or K562mbIL15‐41BBL. Clinical‐grade manufactured NKAE cells complied with the specifications from the Spanish Regulatory Agency. Conclusions: GMP‐grade NK cells for clinical use can be obtained by using different starting cells and aAPCThis work was supported by the National Health Service of Spain, Instituto de Salud Carlos III (ISCIII), FONDOS FEDER grant (FIS) PI18/01301 to Pérez-Martínez A, CRIS Foundation to Beat Cancer to Escudero A, Fernández A; Navarro A, Mirones I, and Fundación Mari Paz Jiménez Casado and La Sonrisa de Álex to Vela

Dynamic soluble changes in sVEGFR1, HGF, and VEGF promote chemotherapy and bevacizumab resistance: A prospective translational study in the BECOX (GEMCAD 09-01) trial

Despite initial responsiveness, acquired resistance to both bevacizumab and chemotherapy in metastatic colorectal cancer is universal. We have recently published that in vitro, chronically oxaliplatin resistance upregulates soluble vascular endothelial growth factor receptor 1, downregulates vascular endothelial growth factor, and also promotes c-MET, b-ca catenin/transcription factor 4, and AKT activation. We tested whether variation in three serum biomarkers such as the natural c-MET ligand (hepatocyte growth factor), soluble vascular endothelial growth factor receptor 1, and vascular endothelial growth factor-A was associated with efficacy in metastatic colorectal cancer patients treated in the prospective BECOX study. Serum levels of vascular endothelial growth factor-A165, soluble vascular endothelial growth factor receptor 1, and hepatocyte growth factor were assessed by enzyme-linked immunosorbent assay method basally and every 3 cycles (at the time of computed tomography evaluation) in a preplanned translational study in the first-line BECOX trial in metastatic colorectal cancer patients treated with CAPOX plus bevacizumab. Response was evaluated by routine contrast-enhanced computed tomography by RECIST 1.1 by investigator assessment and by three blinded independent radiologists. Ratios between soluble vascular endothelial growth factor receptor 1/vascular endothelial growth factor-A and hepatocyte growth factor/vascular endothelial growth factor-A were established and variations through time were related to RECIST 1.1 by investigator assessment and independent radiologist. The BECOX trial included 68 patients, and 27 patients were analyzed in the translational trial. A total of 80 RECIST 1.1 evaluations were done by investigator assessment and 56 by independent radiologist. We found that a 3.22-fold increase in soluble vascular endothelial growth factor receptor 1/vascular endothelial growth factor-A by investigator assessment and a 3.06-fold increase in soluble vascular endothelial growth factor receptor 1/vascular endothelial growth factor-A by independent radiologist from previous determination were associated with responses compared with 1.38-fold increase by investigator assessment and 1.59 by independent radiologist in non-responders (p= 0.0009 and p = 0.03, respectively). Responders had a 3.36-fold increase in hepatocyte growth factor/vascular endothelial growth factor-A from previous determination by investigator assessment and 3.66-fold increase in hepatocyte growth factor/vascular endothelial growth factor-A by independent radiologist compared with 1.43-fold increase by investigator assessment and 1.53 by independent radiologist for non-responders (p = 0.002 and 0.003, respectively). In conclusion, a decrease in vascular endothelial growth factor-A and an increase in soluble vascular endothelial growth factor receptor 1 during chemotherapy and bevacizumab exposure can contribute to both chemotherapy (due to c- MET/b-catenin activation) and bevacizumab (due to low vascular endothelial growth factor requirements) resistance. Because hepatocyte growth factor levels decrease also during acquired resistance, alternative strategies to hepatocyte growth factor–ligand inhibition should be investigatedThis work was supported by “beca SEOM a Jóvenes Investigadores 2009” and by the Emili Letang fellowship to Estela Pineda

Cognitive-motivational psychoeducational intervention in the Learning Acceleration Model

El estudio se desarrolla desde la metodología investigación-acción en educación, y corresponde a un proceso de intervención psicoeducativa que busca favorecer la dimensión cognitivo - motivacional en estudiantes en condición de extra edad del grado aceleración del aprendizaje. Después de la identificación de las necesidades del grupo y el diagnóstico cognitivo motivacional, se estableció como objetivo incrementar el nivel motivacional general de los participantes del estudio por medio de un programa psicoeducativo basado en la teoría motivacional de Pintrich. Este estudio se elaboró a través de 4 fases desde el modelo de Stringer: detección del problema, elaboración del plan, implementaciónevaluación y retroalimentación. Para determinar la efectividad del programa se empleó un diseño preexperimental preprueba/posprueba con un solo grupo preestablecido. El resultado de la prueba de rangos con signo de Wilcoxon fue de 0,32E-4 por debajo del nivel de significancia P<0,05, evidenciándose una diferencia significativa en las medias del puntaje obtenido antes y después del programa psicoeducativo. La magnitud del efecto por medio de la d de Cohen, identifica un nivel grande de efectividad, d=6,81 con respecto al programa diseñado y aplicado. Los participantes aumentaron su nivel de motivación general, desde un nivel bajo predominante en la preprueba (65,2 %) a un nivel alto predominante en la posprueba (87 %). Se puede concluir que se logró el objetivo general de la investigación aplicada incrementando por medios intrínsecos al programa formativo los niveles cognitivo-motivacionales, fortaleciendo la autorregulación, la autoestima y la permanencia de los estudiantes en el sistema educativo.The presented study is developed from the research action methodology in education and corresponds to a process of psychoeducational intervention that seeks to favor the cognitive-motivational dimension in students in a condition of extra age of the degree acceleration of learning. After the identification of the group’s needs and the motivational cognitive diagnosis, the objective was to increase the general motivational level of the study participants through a psychoeducational program based on Pintrich’s motivational theory. This study was carried out through 4 phases from the Stringer model: problem detection, plan development, implementation-evaluation, and feedback. To determine the effectiveness of the program, a pre-test/post-test pre-experimental design with a single pre-established group was used. The result of the Wilcoxon signed-rank test was 0.32E-4 below the significance level P<0.05, showing a significant difference in the means of the score obtained before and after the psychoeducational program. The magnitude of the effect using Cohen’s d identifies a large level of effectiveness, d = 6.81 with respect to the program designed and applied. Participants increased their general motivation level, from a low level prevailing in the pre-test (65.2 %) to a high level prevailing in the post-test (87 %). It can be concluded that the general objective of applied research was achieved by increasing cognitive-motivational levels by intrinsic means to the training program, strengthening selfregulation, self-esteem, and the permanence of students in the educational system

Chikungunya Outbreak in the Republic of the Congo, 2019—Epidemiological, Virological and Entomological Findings of a South-North Multidisciplinary Taskforce Investigation

The Republic of Congo (RoC) declared a chikungunya (CHIK) outbreak on 9 February 2019. We conducted a ONE-Human-Animal HEALTH epidemiological, virological and entomological investigation. Methods: We collected national surveillance and epidemiological data. CHIK diagnosis was based on RT-PCR and CHIKV-specific antibodies. Full CHIKV genome sequences were obtained by Sanger and MinION approaches and Bayesian tree phylogenetic analysis was performed. Mosquito larvae and 215 adult mosquitoes were collected in different villages of Kouilou and Pointe-Noire districts and estimates of Aedes (Ae.) mosquitos’ CHIKV-infectious bites obtained. We found two new CHIKV sequences of the East/Central/South African (ECSA) lineage, clustering with the recent enzootic sub-clade 2, showing the A226V mutation. The RoC 2019 CHIKV strain has two novel mutations, E2-T126M and E2-H351N. Phylogenetic suggests a common origin from 2016 Angola strain, from which it diverged around 1989 (95% HPD 1985–1994). The infectious bite pattern was similar for 2017, 2018 and early 2019. One Ae. albopictus pool was RT-PCR positive. The 2019 RoC CHIKV strain seems to be recently introduced or be endemic in sylvatic cycle. Distinct from the contemporary Indian CHIKV isolates and in contrast to the original Central-African strains (transmitted by Ae. aegypti), it carries the A226V mutation, indicating an independent adaptive mutation in response to vector replacement (Ae. albopictus vs Ae. aegypti)

Oral fosfomycin for the treatment of lower urinary tract infections among kidney transplant recipients—Results of a Spanish multicenter cohort

Preliminary results of this study were presented at the 29th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), held in Amsterdam, The Netherlands, from 13 to 16 April, 2019 (oral communication O‐0699).Oral fosfomycin may constitute an alternative for the treatment of lower urinary tract infections (UTIs) in kidney transplant recipients (KTRs), particularly in view of recent safety concerns with fluroquinolones. Specific data on the efficacy and safety of fosfomycin in KTR are scarce. We performed a retrospective study in 14 Spanish hospitals including KTRs treated with oral fosfomycin (calcium and trometamol salts) for posttransplant cystitis between January 2005 and December 2017. A total of 133 KTRs developed 143 episodes of cystitis. Most episodes (131 [91.6%]) were produced by gram‐negative bacilli (GNB), and 78 (54.5%) were categorized as multidrug resistant (including extended‐spectrum β‐lactamase‐producing Enterobacteriaceae [14%] or carbapenem‐resistant GNB [3.5%]). A median daily dose of 1.5 g of fosfomycin (interquartile range [IQR]: 1.5‐2) was administered for a median of 7 days (IQR: 3‐10). Clinical cure (remission of UTI‐attributable symptoms at the end of therapy) was achieved in 83.9% (120/143) episodes. Among those episodes with follow‐up urine culture, microbiological cure at month 1 was achieved in 70.2% (59/84) episodes. Percutaneous nephrostomy was associated with a lower probability of clinical cure (adjusted odds ratio: 10.50; 95% confidence interval: 0.98‐112.29; P = 0.052). In conclusion, fosfomycin is an effective orally available alternative for treating cystitis among KTRs.This study was supported by Plan Nacional de I+D+i 2013‐2016 and Instituto de Salud Carlos III, Subdirección General de Redes y Centros de Investigación Cooperativa, Ministerio de Ciencia, Innovación y Universidades, Spanish Network for Research in Infectious Diseases (REIPI RD16/0016)—cofinanced by the European Development Regional Fund “A way to achieve Europe”; the Group for Study of Infection in Transplantation and the Immunocompromised Host (GESITRA‐IC) of the Spanish Society of Clinical Microbiology and Infectious Diseases (SEIMC); and the Spanish Network for Research in Renal Diseases (REDInREN RD16/0009). MFR holds a research contract “Miguel Servet” (CP 18/00073) from the Spanish Ministry of Science, Innovation and Universities, Instituto de Salud Carlos III

Predicting Spatial Patterns of Plant Recruitment Using Animal-Displacement Kernels

For plants dispersed by frugivores, spatial patterns of recruitment are primarily influenced by the spatial arrangement and characteristics of parent plants, the digestive characteristics, feeding behaviour and movement patterns of animal dispersers, and the structure of the habitat matrix. We used an individual-based, spatially-explicit framework to characterize seed dispersal and seedling fate in an endangered, insular plant-disperser system: the endemic shrub Daphne rodriguezii and its exclusive disperser, the endemic lizard Podarcis lilfordi. Plant recruitment kernels were chiefly determined by the disperser's patterns of space utilization (i.e. the lizard's displacement kernels), the position of the various plant individuals in relation to them, and habitat structure (vegetation cover vs. bare soil). In contrast to our expectations, seed gut-passage rate and its effects on germination, and lizard speed-of-movement, habitat choice and activity rhythm were of minor importance. Predicted plant recruitment kernels were strongly anisotropic and fine-grained, preventing their description using one-dimensional, frequency-distance curves. We found a general trade-off between recruitment probability and dispersal distance; however, optimal recruitment sites were not necessarily associated to sites of maximal adult-plant density. Conservation efforts aimed at enhancing the regeneration of endangered plant-disperser systems may gain in efficacy by manipulating the spatial distribution of dispersers (e.g. through the creation of refuges and feeding sites) to create areas favourable to plant recruitment