32 results on '"Torres, F."'
Search Results
2. Aeolian transport of viable microbial life across the Atacama Desert, Chile: Implications for Mars
- Author
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Azua-Bustos, Armando, González-Silva, Carlos, Fernández-Martínez, Miguel Ángel, Arenas-Fajardo, Cristián, Fonseca, Ricardo, Martín-Torres, F. Javier, Fernández-Sampedro, Maite, Fairén, Alberto G., and Zorzano, María-Paz
- Published
- 2019
- Full Text
- View/download PDF
3. Tensor Algebra-based Geometrical (3D) Biomacro-Molecular Descriptors for Protein Research: Theory, Applications and Comparison with other Methods
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Terán, Julio E., Marrero-Ponce, Yovani, Contreras-Torres, Ernesto, García-Jacas, César R., Vivas-Reyes, Ricardo, Terán, Enrique, and Torres, F. Javier
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- 2019
- Full Text
- View/download PDF
4. Discovery of recurring slope lineae candidates in Mawrth Vallis, Mars
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Bhardwaj, Anshuman, Sam, Lydia, Martín-Torres, F. Javier, and Zorzano, María-Paz
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- 2019
- Full Text
- View/download PDF
5. Heterogeneity in topographic control on velocities of Western Himalayan glaciers
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Sam, Lydia, Bhardwaj, Anshuman, Kumar, Rajesh, Buchroithner, Manfred F., and Martín-Torres, F. Javier
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- 2018
- Full Text
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6. A 2-transcript host cell signature distinguishes viral from bacterial diarrhea and it is influenced by the severity of symptoms
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Barral-Arca, R., Pardo-Seco, J., Martinón-Torres, F., and Salas, A.
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- 2018
- Full Text
- View/download PDF
7. Author Correction: Aeolian transport of viable microbial life across the Atacama Desert, Chile: Implications for Mars
- Author
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Azua-Bustos, Armando, primary, González-Silva, Carlos, additional, Fernández-Martínez, Miguel Ángel, additional, Arenas-Fajardo, Cristián, additional, Fonseca, Ricardo, additional, Martín-Torres, F. Javier, additional, Fernández-Sampedro, Maite, additional, Fairén, Alberto G., additional, and Zorzano, María-Paz, additional
- Published
- 2020
- Full Text
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8. Martian slope streaks as plausible indicators of transient water activity
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Bhardwaj, Anshuman, Sam, Lydia, Martín-Torres, F. J., Zorzano, María Paz, Fonseca, Ricardo M., NASA Jet Propulsion Laboratory, and German Academic Exchange Service
- Subjects
Science ,Medicine ,Article - Abstract
Slope streaks have been frequently observed in the equatorial, low thermal inertia and dusty regions of Mars. The reason behind their formation remains unclear with proposed hypotheses for both dry and wet mechanisms. Here, we report an up-to-date distribution and morphometric investigation of Martian slope streaks. We find: (i) a remarkable coexistence of the slope streak distribution with the regions on Mars with high abundances of water-equivalent hydrogen, chlorine, and iron; (ii) favourable thermodynamic conditions for transient deliquescence and brine development in the slope streak regions; (iii) a significant concurrence of slope streak distribution with the regions of enhanced atmospheric water vapour concentration, thus suggestive of a present-day regolith-atmosphere water cycle; and (iv) terrain preferences and flow patterns supporting a wet mechanism for slope streaks. These results suggest a strong local regolith-atmosphere water coupling in the slope streak regions that leads to the formation of these fluidised features. Our conclusions can have profound astrobiological, habitability, environmental, and planetary protection implications., We thank NASA/JPL/University of Arizona/Malin Space Science systems/Arizona State University for providing the Gamma Ray Spectrometer (GRS) data, HiRISE images, ConTeXt Camera (CTX) images, LROC images, and JMARS software free of charge. Although we have cited all the previous research results used in the paper, here we acknowledge the efforts of all those researchers for providing the essential inputs to our study. L.S. acknowledges German Academic Exchange Service (DAAD) for her PhD scholarship.
- Published
- 2017
9. Phylogeographic and genome-wide investigations of Vietnam ethnic groups reveal signatures of complex historical demographic movements
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Pischedda, S., primary, Barral-Arca, R., additional, Gómez-Carballa, A., additional, Pardo-Seco, J., additional, Catelli, M. L., additional, Álvarez-Iglesias, V., additional, Cárdenas, J. M., additional, Nguyen, N. D., additional, Ha, H. H., additional, Le, A. T., additional, Martinón-Torres, F., additional, Vullo, C., additional, and Salas, A., additional
- Published
- 2017
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10. Himalayan glaciers experienced significant mass loss during later phases of little ice age
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Shekhar, Mayank, primary, Bhardwaj, Anshuman, additional, Singh, Shaktiman, additional, Ranhotra, Parminder S., additional, Bhattacharyya, Amalava, additional, Pal, Ashish K., additional, Roy, Ipsita, additional, Martín-Torres, F. Javier, additional, and Zorzano, María-Paz, additional
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- 2017
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11. Polyphasic identification of Rhizopus oryzae and evaluation of physical fermentation parameters in potato starch processing liquid waste for β-glucan production.
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Anchundia M, León-Revelo G, Santacruz S, and Torres F
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- Hydrogen-Ion Concentration, Rhizopus metabolism, Temperature, beta-Glucans metabolism, Solanum tuberosum microbiology, Solanum tuberosum metabolism, Starch metabolism, Fermentation, Rhizopus oryzae metabolism
- Abstract
Β-glucans are polysaccharide macromolecules that can be found in the cell walls of molds, such as Rhizopus oryzae. They provide functional properties in food systems and have immunomodulatory activity, anticancer, and prebiotic effects; reduce triglycerides and cholesterol; and prevent obesity, among others benefits. Furthermore, potato starch production requires a large amount of water, which is usually discharged into the environment, creating problems in soils and bodies of water. The physical parameters to produce β-glucans were determined, liquid waste from potato starch processing was used and native Rhizopus oryzae was isolated and identified from cereal grains. The isolates grew quickly on the three types of agars used at 25 °C and 37 °C, and they did not grow at 45 °C. Rhizopus oryzae M10A1 produced the greatest amount of β-glucans after six days of culture at 30 °C, pH 6, a stirring rate of 150 rpm and a fermentation volume of 250 mL. By establishing the physical fermentation parameters and utilizing the liquid waste from potato starch, Rhizopus oryzae M10A1 yielded 397.50 mg/100 g of β-glucan was obtained., (© 2024. The Author(s).)
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- 2024
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12. 3D-printed low-cost choke corrugated Gaussian profile horn antenna for Ka-band.
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Zárate YD, Torres F, Rodriguez M, and Pizarro F
- Abstract
In this work, a fully 3D-printed choke corrugated Gaussian profile horn antenna (GPHA) using high-conductive filaments and a low-cost modular 3D-printing technique is implemented. The choke corrugated GPHA operates in the Ka-band, with a central frequency of 28 GHz. Although the antenna can be printed in one piece as its dimensions are within the printing limits, four pieces compose the three sections of the final 3D-printed antenna. The numerical simulations and measurements of the antenna show a good agreement, validating the possibility of cost-effective modular fabrication of this complex type of antennas., (© 2023. The Author(s).)
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- 2023
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13. Music compensates for altered gene expression in age-related cognitive disorders.
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Gómez-Carballa A, Navarro L, Pardo-Seco J, Bello X, Pischedda S, Viz-Lasheras S, Camino-Mera A, Currás MJ, Ferreirós I, Mallah N, Rey-Vázquez S, Redondo L, Dacosta-Urbieta A, Caamaño-Viña F, Rivero-Calle I, Rodriguez-Tenreiro C, Martinón-Torres F, and Salas A
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- Humans, Cohort Studies, Gene Expression, Music psychology, Cognition Disorders, Cognitive Dysfunction genetics, Cognitive Dysfunction psychology, Alzheimer Disease genetics, Alzheimer Disease psychology
- Abstract
Extensive literature has explored the beneficial effects of music in age-related cognitive disorders (ACD), but limited knowledge exists regarding its impact on gene expression. We analyzed transcriptomes of ACD patients and healthy controls, pre-post a music session (n = 60), and main genes/pathways were compared to those dysregulated in mild cognitive impairment (MCI) and Alzheimer's disease (AD) as revealed by a multi-cohort study (n = 1269 MCI/AD and controls). Music was associated with 2.3 times more whole-genome gene expression, particularly on neurodegeneration-related genes, in ACD than in controls. Co-expressed gene-modules and pathways analysis demonstrated that music impacted autophagy, vesicle and endosome organization, biological processes commonly dysregulated in MCI/AD. Notably, the data indicated a strong negative correlation between musically-modified genes/pathways in ACD and those dysregulated in MCI/AD. These findings highlight the compensatory effect of music on genes/biological processes affected in MCI/AD, providing insights into the molecular mechanisms underlying the benefits of music on these disorders., (© 2023. The Author(s).)
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- 2023
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14. Effect of a light-darkness cycle on the body weight gain of preterm infants admitted to the neonatal intensive care unit.
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Sánchez-Sánchez M, García TL, Heredia D, Reséndiz I, Cruz L, Santiago J, Rojas-Granados A, Ubaldo-Reyes L, Pérez-Campos-Mayoral L, Pérez-Campos E, Vásquez GS, Moguel JM, Zarate R, García O, Sánchez L, Torres F, Paz A, Elizarraras-Rivas J, Hernández-Huerta MT, and Angeles-Castellanos M
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- Humans, Infant, Newborn, Infant, Infant, Premature, Darkness, Infant, Low Birth Weight, Weight Gain, Intensive Care Units, Neonatal, Infant, Premature, Diseases
- Abstract
The Continuous bright light conditions to which premature infants are subjected while hospitalized in Neonatal Intensive Care Units (NICU) can have deleterious effects in terms of growth and development. This study evaluates the benefits of a light/darkness cycle (LDC) in weight and early hospital discharge from the NICU. Subjects were recruited from three participating institutions in Mexico. Eligible patients (n = 294) were premature infants who were hospitalized in the low-risk and high-risk neonatal units classified as stable. The subjects randomized to the experimental group (n = 150) were allocated to LDC conditions are as follows: light from 07:00 to 19:00 and darkness (25 lx) from 19:00 to 07:00. The control group (n = 144) was kept under normal room light conditions (CBL) 24 h a day. Main outcome was weight gain and the effect of reducing the intensity of nocturnal light in development of premature infants. Infants to the LDC gained weight earlier, compared with those randomized to CBL, and had a significant reduction in length of hospital stay. These results highlight those premature infants subjected to a LDC exhibit improvements in physiological development, favoring earlier weight gain and consequently a decrease in hospital stays. ClinicalTrials.gov; 02/09/2020 ID: NCT05230706., (© 2022. The Author(s).)
- Published
- 2022
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15. Characterisation of the blood RNA host response underpinning severity in COVID-19 patients.
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Jackson H, Rivero Calle I, Broderick C, Habgood-Coote D, D'Souza G, Nichols S, Vito O, Gómez-Rial J, Rivero-Velasco C, Rodríguez-Núñez N, Barbeito-Castiñeiras G, Pérez-Freixo H, Barreiro-de Acosta M, Cunnington AJ, Herberg JA, Wright VJ, Gómez-Carballa A, Salas A, Levin M, Martinon-Torres F, and Kaforou M
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- Humans, Immunity, RNA, SARS-CoV-2, Transcriptome, COVID-19
- Abstract
Infection with SARS-CoV-2 has highly variable clinical manifestations, ranging from asymptomatic infection through to life-threatening disease. Host whole blood transcriptomics can offer unique insights into the biological processes underpinning infection and disease, as well as severity. We performed whole blood RNA Sequencing of individuals with varying degrees of COVID-19 severity. We used differential expression analysis and pathway enrichment analysis to explore how the blood transcriptome differs between individuals with mild, moderate, and severe COVID-19, performing pairwise comparisons between groups. Increasing COVID-19 severity was characterised by an abundance of inflammatory immune response genes and pathways, including many related to neutrophils and macrophages, in addition to an upregulation of immunoglobulin genes. In this study, for the first time, we show how immunomodulatory treatments commonly administered to COVID-19 patients greatly alter the transcriptome. Our insights into COVID-19 severity reveal the role of immune dysregulation in the progression to severe disease and highlight the need for further research exploring the interplay between SARS-CoV-2 and the inflammatory immune response., (© 2022. The Author(s).)
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- 2022
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16. The impact of the suppression of highly connected protein interactions on the corona virus infection.
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Torres F, Kiwi M, and Schuller IK
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- Antiviral Agents metabolism, Antiviral Agents pharmacology, Antiviral Agents therapeutic use, COVID-19 Vaccines, Humans, SARS-CoV-2, Viral Proteins metabolism, COVID-19, Influenza A Virus, H1N1 Subtype metabolism, Virus Diseases, Viruses metabolism
- Abstract
Several highly effective Covid-19 vaccines are in emergency use, although more-infectious coronavirus strains, could delay the end of the pandemic even further. Because of this, it is highly desirable to develop fast antiviral drug treatments to accelerate the lasting immunity against the virus. From a theoretical perspective, computational approaches are useful tools for antiviral drug development based on the data analysis of gene expression, chemical structure, molecular pathway, and protein interaction mapping. This work studies the structural stability of virus-host interactome networks based on the graphical representation of virus-host protein interactions as vertices or nodes connected by commonly shared proteins. These graphical network visualization methods are analogous to those use in the design of artificial neural networks in neuromorphic computing. In standard protein-node-based network representation, virus-host interaction merges with virus-protein and host-protein networks, introducing redundant links associated with the internal virus and host networks. On the contrary, our approach provides a direct geometrical representation of viral infection structure and allows the effective and fast detection of the structural robustness of the virus-host network through proteins removal. This method was validated by applying it to H1N1 and HIV viruses, in which we were able to pinpoint the changes in the Interactome Network produced by known vaccines. The application of this method to the SARS-CoV-2 virus-host protein interactome implies that nonstructural proteins nsp4, nsp12, nsp16, the nuclear pore membrane glycoprotein NUP210, and ubiquitin specific peptidase USP54 play a crucial role in the viral infection, and their removal may provide an efficient therapy. This method may be extended to any new mutations or other viruses for which the Interactome Network is experimentally determined. Since time is of the essence, because of the impact of more-infectious strains on controlling the spread of the virus, this method may be a useful tool for novel antiviral therapies., (© 2022. The Author(s).)
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- 2022
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17. Genetic and geographical delineation of zoonotic vector-borne helminths of canids.
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Laidoudi Y, Bedjaoui S, Latrofa MS, Fanelli A, Dantas-Torres F, and Otranto D
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- Animals, Disease Vectors, Genetic Variation, Onchocerca, Phylogeny, Canidae, Dirofilaria immitis, Dirofilaria repens
- Abstract
Several zoonotic vector-borne helminths (VBHs) infesting canids cause serious veterinary and medical diseases worldwide. Increasing the knowledge about their genetic structures is pivotal to identify them and therefore to settle effective surveillance and control measures. To overcome the limitation due to the heterogeneity of large DNA sequence-datasets used for their genetic characterization, available cytochrome c oxidase subunit 1 (cox1) (n = 546) and the 12S rRNA (n = 280) sequences were examined using combined bioinformatic approach (i.e., distance-clustering, maximum likelihood phylogeny and phylogenetic evolutionary placement). Out of the 826 DNA available sequences from GenBank, 94.7% were characterized at the haplotype level regardless sequence size, completeness and/or their position. A total of 89 different haplotypes were delineated either by cox1 (n = 35), 12S rRNA (n = 21) or by both genes (n = 33), for 14 VBHs (e.g., Acanthocheilonema reconditum, Brugia spp., Dirofilaria immitis, Dirofilaria repens, Onchocerca lupi and Thelazia spp.). Overall, the present approach could be useful for studying global genetic diversity and phylogeography of VBHs. However, as barcoding sequences were restricted to two mitochondrial loci (cox1 and 12S rRNA), the haplotype delineation proposed herein should be confirmed by the characterization of other nuclear loci also to overcome potential limitations caused by the heteroplasmy phenomenon within the mitogenome of VBHs., (© 2022. The Author(s).)
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- 2022
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18. MiR-195 enhances cardiomyogenic differentiation of the proepicardium/septum transversum by Smurf1 and Foxp1 modulation.
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Dueñas A, Expósito A, Muñoz MDM, de Manuel MJ, Cámara-Morales A, Serrano-Osorio F, García-Padilla C, Hernández-Torres F, Domínguez JN, Aránega A, and Franco D
- Subjects
- Animals, Cell Lineage, Chick Embryo, Gene Expression Regulation, Developmental, Pericardium cytology, Cell Differentiation, Forkhead Transcription Factors metabolism, MicroRNAs genetics, Myocytes, Cardiac cytology, Pericardium embryology, Ubiquitin-Protein Ligases metabolism
- Abstract
Cardiovascular development is a complex developmental process in which multiple cell lineages are involved, namely the deployment of first and second heart fields. Beside the contribution of these cardiogenic fields, extracardiac inputs to the developing heart are provided by the migrating cardiac neural crest cells and the proepicardial derived cells. The proepicardium (PE) is a transitory cauliflower-like structure located between the cardiac and hepatic primordia. The PE is constituted by an internal mesenchymal component surrounded by an external epithelial lining. With development, cells derived from the proepicardium migrate to the neighboring embryonic heart and progressive cover the most external surface, leading to the formation of the embryonic epicardium. Experimental evidence in chicken have nicely demonstrated that epicardial derived cells can distinctly contribute to fibroblasts, endothelial and smooth muscle cells. Surprisingly, isolation of the developing PE anlage and ex vivo culturing spontaneously lead to differentiation into beating cardiomyocytes, a process that is enhanced by Bmp but halted by Fgf administration. In this study we provide a comprehensive characterization of the developmental expression profile of multiple microRNAs during epicardial development in chicken. Subsequently, we identified that miR-125, miR-146, miR-195 and miR-223 selectively enhance cardiomyogenesis both in the PE/ST explants as well as in the embryonic epicardium, a Smurf1- and Foxp1-driven process. In addition we identified three novel long non-coding RNAs with enhanced expression in the PE/ST, that are complementary regulated by Bmp and Fgf administration and well as by microRNAs that selectively promote cardiomyogenesis, supporting a pivotal role of these long non coding RNAs in microRNA-mediated cardiomyogenesis of the PE/ST cells.
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- 2020
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19. Experimental infections and co-infections with Leishmania braziliensis and Leishmania infantum in two sand fly species, Lutzomyia migonei and Lutzomyia longipalpis.
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Alexandre J, Sadlova J, Lestinova T, Vojtkova B, Jancarova M, Podesvova L, Yurchenko V, Dantas-Torres F, Brandão-Filho SP, and Volf P
- Subjects
- Animals, Digestive System parasitology, Female, Leishmania braziliensis growth & development, Leishmania infantum growth & development, Life Cycle Stages, Insect Vectors parasitology, Leishmania braziliensis physiology, Leishmania infantum physiology, Psychodidae parasitology
- Abstract
Leishmaniases are neglected tropical diseases and Leishmania (Leishmania) infantum and Leishmania (Viannia) braziliensis are the most important causative agents of leishmaniases in the New World. These two parasite species may co-circulate in a given endemic area but their interactions in the vector have not been studied yet. We conducted experimental infections using both single infections and co-infections to compare the development of L. (L.) infantum (OGVL/mCherry) and L. (V.) braziliensis (XB29/GFP) in Lutzomyia longipalpis and Lutzomyia migonei. Parasite labelling by different fluorescein proteins enabled studying interspecific competition and localization of different parasite species during co-infections. Both Leishmania species completed their life cycle, producing infective forms in both sand fly species studied. The same happens in the co infections, demonstrating that the two parasites conclude their development and do not compete with each other. However, infections produced by L. (L.) infantum reached higher rates and grew more vigorously, as compared to L. (V.) braziliensis. In late-stage infections, L. (L.) infantum was present in all midgut regions, showing typical suprapylarian type of development, whereas L. (V.) braziliensis was concentrated in the hindgut and the abdominal midgut (peripylarian development). We concluded that both Lu. migonei and Lu. longipalpis are equally susceptible vectors for L. (L.) infantum, in laboratory colonies. In relation to L. (V.) braziliensis, Lu. migonei appears to be more susceptible to this parasite than Lu. longipalpis.
- Published
- 2020
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20. Plasma lipid profiles discriminate bacterial from viral infection in febrile children.
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Wang X, Nijman R, Camuzeaux S, Sands C, Jackson H, Kaforou M, Emonts M, Herberg JA, Maconochie I, Carrol ED, Paulus SC, Zenz W, Van der Flier M, de Groot R, Martinon-Torres F, Schlapbach LJ, Pollard AJ, Fink C, Kuijpers TT, Anderson S, Lewis MR, Levin M, and McClure M
- Subjects
- Adolescent, Bacterial Infections diagnosis, Biomarkers blood, Child, Child, Preschool, Diagnosis, Differential, Female, Fever of Unknown Origin diagnosis, Humans, Infant, Male, Virus Diseases diagnosis, Bacterial Infections blood, Cholesterol blood, Fever of Unknown Origin blood, Inositol Phosphates blood, Lysophosphatidylcholines blood, Sphingomyelins blood, Virus Diseases blood
- Abstract
Fever is the most common reason that children present to Emergency Departments. Clinical signs and symptoms suggestive of bacterial infection are often non-specific, and there is no definitive test for the accurate diagnosis of infection. The 'omics' approaches to identifying biomarkers from the host-response to bacterial infection are promising. In this study, lipidomic analysis was carried out with plasma samples obtained from febrile children with confirmed bacterial infection (n = 20) and confirmed viral infection (n = 20). We show for the first time that bacterial and viral infection produces distinct profile in the host lipidome. Some species of glycerophosphoinositol, sphingomyelin, lysophosphatidylcholine and cholesterol sulfate were higher in the confirmed virus infected group, while some species of fatty acids, glycerophosphocholine, glycerophosphoserine, lactosylceramide and bilirubin were lower in the confirmed virus infected group when compared with confirmed bacterial infected group. A combination of three lipids achieved an area under the receiver operating characteristic (ROC) curve of 0.911 (95% CI 0.81 to 0.98). This pilot study demonstrates the potential of metabolic biomarkers to assist clinicians in distinguishing bacterial from viral infection in febrile children, to facilitate effective clinical management and to the limit inappropriate use of antibiotics.
- Published
- 2019
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21. A qPCR expression assay of IFI44L gene differentiates viral from bacterial infections in febrile children.
- Author
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Gómez-Carballa A, Cebey-López M, Pardo-Seco J, Barral-Arca R, Rivero-Calle I, Pischedda S, Currás-Tuala MJ, Gómez-Rial J, Barros F, Martinón-Torres F, and Salas A
- Subjects
- Bacterial Infections genetics, Bacterial Infections physiopathology, Biomarkers metabolism, Child, Child, Preschool, Diagnosis, Differential, Female, Gene Expression Profiling, Humans, Infant, Male, Real-Time Polymerase Chain Reaction, Seizures, Febrile genetics, Seizures, Febrile physiopathology, Transcriptome genetics, Virus Diseases genetics, Bacterial Infections diagnosis, Seizures, Febrile diagnosis, Tumor Suppressor Proteins genetics, Virus Diseases diagnosis
- Abstract
The diagnosis of bacterial infections in hospital settings is currently performed using bacterial culture from sterile site, but they are lengthy and limited. Transcriptomic biomarkers are becoming promising tools for diagnosis with potential applicability in clinical settings. We evaluated a RT-qPCR assay for a 2-transcript host expression signature (FAM89A and IFI44L genes) inferred from microarray data that allow to differentiate between viral and bacterial infection in febrile children. This assay was able to discriminate viral from bacterial infections (P-value = 1.04 × 10
-4 ; AUC = 92.2%; sensitivity = 90.9%; specificity = 85.7%) and showed very high reproducibility regardless of the reference gene(s) used to normalize the data. Unexpectedly, the monogenic IFI44L expression signature yielded better results than those obtained from the 2-transcript test (P-value = 3.59 × 10-5 ; AUC = 94.1%; sensitivity = 90.9%; specificity = 92.8%). We validated this IFI44L signature in previously published microarray and whole-transcriptome data from patients affected by different types of viral and bacterial infections, confirming that this gene alone differentiates between both groups, thus saving time, effort, and costs. Herein, we demonstrate that host expression microarray data can be successfully translated into a fast, highly accurate and relatively inexpensive in vitro assay that could be implemented in the clinical routine.- Published
- 2019
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22. Identification of regulatory variants associated with genetic susceptibility to meningococcal disease.
- Author
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Borghini L, Png E, Binder A, Wright VJ, Pinnock E, de Groot R, Hazelzet J, Emonts M, Van der Flier M, Schlapbach LJ, Anderson S, Secka F, Salas A, Fink C, Carrol ED, Pollard AJ, Coin LJ, Kuijpers TW, Martinon-Torres F, Zenz W, Levin M, Hibberd ML, and Davila S
- Subjects
- Case-Control Studies, Cohort Studies, Genetic Association Studies, Genomics, High-Throughput Nucleotide Sequencing, Humans, Hypopharyngeal Neoplasms microbiology, Hypopharyngeal Neoplasms pathology, Meningococcal Infections epidemiology, Meningococcal Infections microbiology, Neisseria meningitidis isolation & purification, Phenotype, Tumor Cells, Cultured, Genetic Predisposition to Disease, Hypopharyngeal Neoplasms genetics, Meningococcal Infections genetics, Neisseria meningitidis genetics, Polymorphism, Single Nucleotide, Regulatory Sequences, Nucleic Acid
- Abstract
Non-coding genetic variants play an important role in driving susceptibility to complex diseases but their characterization remains challenging. Here, we employed a novel approach to interrogate the genetic risk of such polymorphisms in a more systematic way by targeting specific regulatory regions relevant for the phenotype studied. We applied this method to meningococcal disease susceptibility, using the DNA binding pattern of RELA - a NF-kB subunit, master regulator of the response to infection - under bacterial stimuli in nasopharyngeal epithelial cells. We designed a custom panel to cover these RELA binding sites and used it for targeted sequencing in cases and controls. Variant calling and association analysis were performed followed by validation of candidate polymorphisms by genotyping in three independent cohorts. We identified two new polymorphisms, rs4823231 and rs11913168, showing signs of association with meningococcal disease susceptibility. In addition, using our genomic data as well as publicly available resources, we found evidences for these SNPs to have potential regulatory effects on ATXN10 and LIF genes respectively. The variants and related candidate genes are relevant for infectious diseases and may have important contribution for meningococcal disease pathology. Finally, we described a novel genetic association approach that could be applied to other phenotypes.
- Published
- 2019
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23. Paternal leakage and mtDNA heteroplasmy in Rhipicephalus spp. ticks.
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Mastrantonio V, Latrofa MS, Porretta D, Lia RP, Parisi A, Iatta R, Dantas-Torres F, Otranto D, and Urbanelli S
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- Animals, Crosses, Genetic, DNA, Mitochondrial genetics, Female, Male, Mitochondria genetics, Multiplex Polymerase Chain Reaction veterinary, Paternal Inheritance, RNA, Ribosomal genetics, Rhipicephalus genetics
- Abstract
Paternal leakage of mitochondrial DNA (mtDNA) and heteroplasmy have been recently described in several animal species. In arthropods, by searching in the Scopus database, we found only 23 documented cases of paternal leakage. Therefore, although arthropods represent a large fraction of animal biodiversity, this phenomenon has been investigated only in a paucity of species in this phylum, thus preventing a reliable estimate of its frequency. Here, we investigated the occurrence of paternal leakage and mtDNA heteroplasmy in ticks belonging to one of the most significant tick species complexes, the so-called Rhipicephalus sanguineus sensu lato. By developing a multiplex allele-specific PCR assay targeting a fragment of the 12S rRNA ribosomal region of the mtDNA, we showed the occurrence of paternal leakage and mtDNA heteroplasmy in R. sanguineus s.l. ticks originated from experimental crosses, as well as in individuals collected from the field. Our results add a new evidence of paternal leakage in arthropods and document for the first time this phenomenon in ticks. Furthermore, they suggest the importance of using allele-specific assays when searching for paternal leakage and/or heteroplasmy, as standard sequencing methods may fail to detect the rare mtDNA molecules.
- Published
- 2019
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24. Author Correction: Nucleation of superfluid-light domains in a quenched dynamics.
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Figueroa J, Rogan J, Valdivia JA, Kiwi M, Romero G, and Torres F
- Abstract
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
- Published
- 2018
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25. The Stochastic Transport Dynamics of a Conserved Quantity on a Complex Network.
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Medina P, Clark J, Kiwi M, Torres F, Rogan J, and Valdivia JA
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- Computer Simulation, Models, Theoretical, Stochastic Processes
- Abstract
The stochastic dynamics of conserved quantities is an emergent phenomena observed in many complex systems, ranging from social and to biological networks. Using an extension of the Ehrenfest urn model on a complex network, over which a conserved quantity is transported in a random fashion, we study the dynamics of many elementary packets transported through the network by means of a master equation approach and compare with the mean field approximation and stochastic simulations. By use of the mean field theory, it is possible to compute an approximation to the ensemble average evolution of the number of packets in each node which, in the thermodynamic limit, agrees quite well with the results of the master equation. However, the master equation gives a more complete description of the stochastic system and provides a probabilistic view of the occupation number at each node. Of particular relevance is the standard deviation of the occupation number at each node, which is not uniform for a complex network. We analyze and compare different network topologies (small world, scale free, Erdos-Renyi, among others). Given the computational complexity of directly evaluating the asymptotic, or equilibrium, occupation number probability distribution, we propose a scaling relation with the number of packets in the network, that allows to construct the asymptotic probability distributions from the network with one packet. The approximation, which relies on the same matrix found in the mean field approach, becomes increasingly more accurate for a large number of packets.
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- 2018
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26. Nucleation of superfluid-light domains in a quenched dynamics.
- Author
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Figueroa J, Rogan J, Valdivia JA, Kiwi M, Romero G, and Torres F
- Abstract
Strong correlation effects emerge from light-matter interactions in coupled resonator arrays, such as the Mott-insulator to superfluid phase transition of atom-photon excitations. We demonstrate that the quenched dynamics of a finite-sized complex array of coupled resonators induces a first-order like phase transition. The latter is accompanied by domain nucleation that can be used to manipulate the photonic transport properties of the simulated superfluid phase; this in turn leads to an empirical scaling law. This universal behavior emerges from the light-matter interaction and the topology of the array. The validity of our results over a wide range of complex architectures might lead to a promising device for use in scaled quantum simulations.
- Published
- 2018
- Full Text
- View/download PDF
27. Whole Exome Sequencing reveals new candidate genes in host genomic susceptibility to Respiratory Syncytial Virus Disease.
- Author
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Salas A, Pardo-Seco J, Cebey-López M, Gómez-Carballa A, Obando-Pacheco P, Rivero-Calle I, Currás-Tuala MJ, Amigo J, Gómez-Rial J, and Martinón-Torres F
- Subjects
- Case-Control Studies, Gene Ontology, Humans, Infant, Infant, Newborn, Polymorphism, Single Nucleotide genetics, Genetic Association Studies, Genetic Predisposition to Disease, Genome, Human, Host-Pathogen Interactions genetics, Respiratory Syncytial Virus Infections genetics, Respiratory Syncytial Virus Infections virology, Respiratory Syncytial Virus, Human physiology, Exome Sequencing
- Abstract
Respiratory syncytial virus (RSV) is an important cause of serious lower respiratory tract disease in infants. Several studies have shown evidence pointing to the genome of the host as an important factor determining susceptibility to respiratory disease caused by RSV. We sequenced the complete exomes of 54 patients infected by RSV that needed hospitalization due to development of severe bronchiolitis. The Iberian sample (IBS) from The 1000 Genomes Project (1000G) was used as control group; all the association results were pseudo-replicated using other 1000G-European controls and Spanish controls. The study points to SNP rs199665292 in the olfactory receptor (OR) gene OR13C5 as the best candidate variant (P-value = 1.16 × 10
-12 ; OR = 5.56). Genetic variants at HLA genes (HLA-DQA1, HLA-DPB1), and in the mucin 4 gene (MUC4) also emerge as susceptibility candidates. By collapsing rare variants in genes and weighing by pathogenicity, we obtained confirmatory signals of association in the OR gene OR8U1/OR8U8, the taste receptor TAS2R19, and another mucin gene (MUC6). Overall, we identified new predisposition variants and genes related to RSV infection. Of special interest is the association of RSV to olfactory and taste receptors; this finding is in line with recent evidence pointing to their role in viral infectious diseases.- Published
- 2017
- Full Text
- View/download PDF
28. ISL1 is a major susceptibility gene for classic bladder exstrophy and a regulator of urinary tract development.
- Author
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Zhang R, Knapp M, Suzuki K, Kajioka D, Schmidt JM, Winkler J, Yilmaz Ö, Pleschka M, Cao J, Kockum CC, Barker G, Holmdahl G, Beaman G, Keene D, Woolf AS, Cervellione RM, Cheng W, Wilkins S, Gearhart JP, Sirchia F, Di Grazia M, Ebert AK, Rösch W, Ellinger J, Jenetzky E, Zwink N, Feitz WF, Marcelis C, Schumacher J, Martinón-Torres F, Hibberd ML, Khor CC, Heilmann-Heimbach S, Barth S, Boyadjiev SA, Brusco A, Ludwig M, Newman W, Nordenskjöld A, Yamada G, Odermatt B, and Reutter H
- Subjects
- Animals, Bladder Exstrophy metabolism, Bladder Exstrophy pathology, Embryo, Mammalian, Female, Gene Expression Regulation, Developmental, Humans, LIM-Homeodomain Proteins metabolism, Larva genetics, Larva growth & development, Larva metabolism, Mesoderm abnormalities, Mesoderm growth & development, Mice, Polymorphism, Single Nucleotide, Pronephros growth & development, Pronephros metabolism, Protein Isoforms genetics, Protein Isoforms metabolism, Transcription Factors metabolism, Urinary Tract abnormalities, Urinary Tract growth & development, Zebrafish, Bladder Exstrophy genetics, Genetic Predisposition to Disease, LIM-Homeodomain Proteins genetics, Mesoderm metabolism, Organogenesis genetics, Transcription Factors genetics, Urinary Tract metabolism
- Abstract
Previously genome-wide association methods in patients with classic bladder exstrophy (CBE) found association with ISL1, a master control gene expressed in pericloacal mesenchyme. This study sought to further explore the genetics in a larger set of patients following-up on the most promising genomic regions previously reported. Genotypes of 12 markers obtained from 268 CBE patients of Australian, British, German Italian, Spanish and Swedish origin and 1,354 ethnically matched controls and from 92 CBE case-parent trios from North America were analysed. Only marker rs6874700 at the ISL1 locus showed association (p = 2.22 × 10
-08 ). A meta-analysis of rs6874700 of our previous and present study showed a p value of 9.2 × 10-19 . Developmental biology models were used to clarify the location of ISL1 activity in the forming urinary tract. Genetic lineage analysis of Isl1-expressing cells by the lineage tracer mouse model showed Isl1-expressing cells in the urinary tract of mouse embryos at E10.5 and distributed in the bladder at E15.5. Expression of isl1 in zebrafish larvae staged 48 hpf was detected in a small region of the developing pronephros. Our study supports ISL1 as a major susceptibility gene for CBE and as a regulator of urinary tract development., Competing Interests: The authors declare no competing financial interests.- Published
- 2017
- Full Text
- View/download PDF
29. Genomic continuity of Argentinean Mennonites.
- Author
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Pardo-Seco J, Llull C, Berardi G, Gómez A, Andreatta F, Martinón-Torres F, Toscanini U, and Salas A
- Subjects
- Argentina, Consanguinity, Genetics, Population, Genome, Human, Humans, Ethnicity genetics, Genotyping Techniques methods, Polymorphism, Single Nucleotide
- Abstract
Mennonites are Anabaptist communities that originated in Central Europe about 500 years ago. They initially migrated to different European countries, and in the early 18
th century they established their first communities in North America, from where they moved to other American regions. We aimed to analyze an Argentinean Mennonite congregation from a genome-wide perspective by way of investigating >580.000 autosomal SNPs. Several analyses show that Argentinean Mennonites have European ancestry without signatures of admixture with other non-European American populations. Among the worldwide datasets used for population comparison, the CEU, which is the best-subrogated Central European population existing in The 1000 Genome Project, is the dataset showing the closest genome affinity to the Mennonites. When compared to other European population samples, the Mennonites show higher inbreeding coefficient values. Argentinean Mennonites show signatures of genetic continuity with no evidence of admixture with Americans of Native American or sub-Saharan African ancestry. Their genome indicates the existence of an increased endogamy compared to other Europeans most likely mirroring their lifestyle that involve small communities and historical consanguineous marriages.- Published
- 2016
- Full Text
- View/download PDF
30. Natural resistance to Meningococcal Disease related to CFH loci: Meta-analysis of genome-wide association studies.
- Author
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Martinón-Torres F, Png E, Khor CC, Davila S, Wright VJ, Sim KS, Vega A, Fachal L, Inwald D, Nadel S, Carrol ED, Martinón-Torres N, Alonso SM, Carracedo A, Morteruel E, López-Bayón J, Torre AC, Monge CC, de Aguilar PA, Torné EE, Martínez-Padilla MD, Martinón-Sánchez JM, Levin M, Hibberd ML, and Salas A
- Subjects
- Databases, Factual, Genetic Loci, Genotype, Humans, Meningococcal Infections pathology, Odds Ratio, Polymorphism, Single Nucleotide, Spain, White People genetics, Complement Factor H genetics, Genome-Wide Association Study, Immunity, Innate, Meningococcal Infections genetics
- Abstract
Meningococcal disease (MD) remains an important infectious cause of life threatening infection in both industrialized and resource poor countries. Genetic factors influence both occurrence and severity of presentation, but the genes responsible are largely unknown. We performed a genome-wide association study (GWAS) examining 5,440,063 SNPs in 422 Spanish MD patients and 910 controls. We then performed a meta-analysis of the Spanish GWAS with GWAS data from the United Kingdom (combined cohorts: 897 cases and 5,613 controls; 4,898,259 SNPs). The meta-analysis identified strong evidence of association (P-value ≤ 5 × 10
-8 ) in 20 variants located at the CFH gene. SNP rs193053835 showed the most significant protective effect (Odds Ratio (OR) = 0.62, 95% confidence interval (C.I.) = 0.52-0.73; P-value = 9.62 × 10-9 ). Five other variants had been previously reported to be associated with susceptibility to MD, including the missense SNP rs1065489 (OR = 0.64, 95% C.I.) = 0.55-0.76, P-value = 3.25 × 10-8 ). Theoretical predictions point to a functional effect of rs1065489, which may be directly responsible for protection against MD. Our study confirms the association of CFH with susceptibility to MD and strengthens the importance of this link in understanding pathogenesis of the disease.- Published
- 2016
- Full Text
- View/download PDF
31. The complete mitogenome of a 500-year-old Inca child mummy.
- Author
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Gómez-Carballa A, Catelli L, Pardo-Seco J, Martinón-Torres F, Roewer L, Vullo C, and Salas A
- Subjects
- Argentina, Child, DNA, Mitochondrial chemistry, DNA, Mitochondrial classification, Haplotypes, Humans, Phylogeny, Religion, Sequence Analysis, DNA, DNA, Mitochondrial genetics, Genome, Mitochondrial genetics, Indians, South American, Mummies
- Abstract
In 1985, a frozen mummy was found in Cerro Aconcagua (Argentina). Archaeological studies identified the mummy as a seven-year-old Inca sacrifice victim who lived >500 years ago, at the time of the expansion of the Inca Empire towards the southern cone. The sequence of its entire mitogenome was obtained. After querying a large worldwide database of mitogenomes (>28,000) we found that the Inca haplotype belonged to a branch of haplogroup C1b (C1bi) that has not yet been identified in modern Native Americans. The expansion of C1b into the Americas, as estimated using 203 C1b mitogenomes, dates to the initial Paleoindian settlements (~18.3 thousand years ago [kya]); however, its internal variation differs between Mesoamerica and South America. By querying large databases of control region haplotypes (>150,000), we found only a few C1bi members in Peru and Bolivia (e.g. Aymaras), including one haplotype retrieved from ancient DNA of an individual belonging to the Wari Empire (Peruvian Andes). Overall, the results suggest that the profile of the mummy represents a very rare sub-clade that arose 14.3 (5-23.6) kya and could have been more frequent in the past. A Peruvian Inca origin for present-day C1bi haplotypes would satisfy both the genetic and paleo-anthropological findings.
- Published
- 2015
- Full Text
- View/download PDF
32. Feline lungworms unlock a novel mode of parasite transmission.
- Author
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Colella V, Giannelli A, Brianti E, Ramos RA, Cantacessi C, Dantas-Torres F, and Otranto D
- Subjects
- Animals, Cats, Larva pathogenicity, Strongylida Infections parasitology, Strongylida Infections transmission, Cat Diseases parasitology, Cat Diseases transmission, Metastrongyloidea pathogenicity, Snails parasitology, Strongylida Infections veterinary
- Abstract
Snail-borne lungworms exert an enormous toll on the health and welfare of animals and humans. Of these parasites, Aelurostrongylus abstrusus and Troglostrongylus brevior affect the respiratory tract of felids. These lungworms share both the ecological niche and the species of snail (Helix aspersa) acting as intermediate host. Recently, the ability of H. aspersa to shed infective third-stage larvae (L3s) of A. abstrusus and T. brevior in the environment has been demonstrated, matching previous knowledge of mode of transmission of zoonotic lungworms. Here, we evaluated, for the first time, the ability of A. abstrusus and T. brevior L3s to infect new, susceptible snail hosts following their release from experimentally infected molluscs, and refer to this novel route of parasite transmission as intermediesis. The implications of snail-to-snail transmission in the epidemiology of snail-borne diseases are also discussed.
- Published
- 2015
- Full Text
- View/download PDF
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