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Martínez-Alvarenga H, Gutiérrez MC, Gómez-Cámer JL, Benítez A, Martín MA, Caballero A. Integral evaluation of effective conversion of sewage sludge from WWTP into highly porous activated carbon. J Environ Manage 2024; 351:119822. [PMID: 38134504 DOI: 10.1016/j.jenvman.2023.119822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/24/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023]
Abstract
Urban sewage sludge (SL) is a major concern due to the number of environmental problems it causes. Its application for different purposes is strictly regulated, limiting the possibilities of recycling and reusing this material. Thus, in this work, a complete study of a simple method to convert SL into activated carbon (AC) was carried out. The comprehensive study involves an evaluation of the main process parameters, such as the activating agent (AA) content (25 %, 33 %, 50 %), using the lowest amount of AA as novelty, different pyrolysis temperatures (600 and 800 °C), and purification conditions (6 M HCl:AC ratio, v:w). Under controlled and optimised conditions and through a single combined activation and pyrolysis step followed by acid purification, ACs with well-developed porosity can be obtained. Surface area values of around 870 m2/g and over 60 % carbon content were achieved, demonstrating that the prepared ACs could have applications in a wide variety of fields as high-value products. As an innovative aspect in this research, the gases streams and liquid effluents generated during the global process were analysed, achieving elimination of over 63 % of the concentration of the chemical elements contained in the SL during the chemical purification stage. Finally, mass, energy, and economic balances were carried out to estimate the production cost of AC derived from SL (<€ 8/kg AC).
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Affiliation(s)
- H Martínez-Alvarenga
- Dpto. Química Inorgánica e Ingeniería Química, Instituto Químico para la Energía y el Medioambiente (IQUEMA), Universidad de Córdoba, 14014, Córdoba, Spain
| | - M C Gutiérrez
- Dpto. Química Inorgánica e Ingeniería Química, Instituto Químico para la Energía y el Medioambiente (IQUEMA), Universidad de Córdoba, 14014, Córdoba, Spain; Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Campus Universitario de Rabanales, N-IV, km 396, Córdoba, 14071, Spain
| | - J L Gómez-Cámer
- Dpto. Química Inorgánica e Ingeniería Química, Instituto Químico para la Energía y el Medioambiente (IQUEMA), Universidad de Córdoba, 14014, Córdoba, Spain
| | - A Benítez
- Dpto. Química Inorgánica e Ingeniería Química, Instituto Químico para la Energía y el Medioambiente (IQUEMA), Universidad de Córdoba, 14014, Córdoba, Spain.
| | - M A Martín
- Dpto. Química Inorgánica e Ingeniería Química, Instituto Químico para la Energía y el Medioambiente (IQUEMA), Universidad de Córdoba, 14014, Córdoba, Spain; Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Campus Universitario de Rabanales, N-IV, km 396, Córdoba, 14071, Spain.
| | - A Caballero
- Dpto. Química Inorgánica e Ingeniería Química, Instituto Químico para la Energía y el Medioambiente (IQUEMA), Universidad de Córdoba, 14014, Córdoba, Spain
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2
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Santiago E, Caballero A, Köpke C, Novo I. Estimation of the contemporary effective population size from SNP data while accounting for mating structure. Mol Ecol Resour 2024; 24:e13890. [PMID: 37937674 DOI: 10.1111/1755-0998.13890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023]
Abstract
A new method is developed to estimate the contemporary effective population size (Ne ) from linkage disequilibrium (LD) between SNPs without information on their location, which is the usual scenario in non-model species. The general theory of linkage disequilibrium is extended to include the contribution of full-sibs to the measure of LD, leading naturally to the estimation of Ne in monogamous and polygamous mating systems, as well as in multiparous species, and with non-random distributions of full-sib family size due to selection or other causes. Prediction of confidence intervals for Ne estimates was solved using a small artificial neural network trained on a dataset of over 105 simulation results. The method, implemented in a user-friendly and fast software (currentNe), is able to estimate Ne even in problematic scenarios with large population sizes or small sample sizes and provides confidence intervals that are more consistent than resampling methods.
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Affiliation(s)
- Enrique Santiago
- Departamento de Biología Funcional, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain
| | - Armando Caballero
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | | | - Irene Novo
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
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3
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Novo I, Ordás P, Moraga N, Santiago E, Quesada H, Caballero A. Impact of population structure in the estimation of recent historical effective population size by the software GONE. Genet Sel Evol 2023; 55:86. [PMID: 38049712 PMCID: PMC10694967 DOI: 10.1186/s12711-023-00859-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Effective population size (Ne) is a crucial parameter in conservation genetics and animal breeding. A recent method, implemented by the software GONE, has been shown to be rather accurate in estimating recent historical changes in Ne from a single sample of individuals. However, GONE estimations assume that the population being studied has remained isolated for a period of time, that is, without migration or confluence of other populations. If this occurs, the estimates of Ne can be heavily biased. In this paper, we evaluate the impact of migration and admixture on the estimates of historical Ne provided by GONE through a series of computer simulations considering several scenarios: (a) the mixture of two or more ancestral populations; (b) subpopulations that continuously exchange individuals through migration; (c) populations receiving migrants from a large source; and (d) populations with balanced systems of chromosomal inversions, which also generate genetic structure. RESULTS Our results indicate that the estimates of historical Ne provided by GONE may be substantially biased when there has been a recent mixture of populations that were previously separated for a long period of time. Similarly, biases may occur when the rate of continued migration between populations is low, or when chromosomal inversions are present at high frequencies. However, some biases due to population structuring can be eliminated by conducting population structure analyses and restricting the estimation to the differentiated groups. In addition, disregarding the genomic regions that are involved in inversions can also remove biases in the estimates of Ne. CONCLUSIONS Different kinds of deviations from isolation and panmixia of the populations can generate biases in the recent historical estimates of Ne. Therefore, estimation of past demography could benefit from performing population structure analyses beforehand, by mitigating the impact of these biases on historical Ne estimates.
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Affiliation(s)
- Irene Novo
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310, Vigo, Spain.
| | - Pilar Ordás
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310, Vigo, Spain
| | - Natalia Moraga
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310, Vigo, Spain
| | - Enrique Santiago
- Departamento de Biología Funcional, Facultad de Biología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Humberto Quesada
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310, Vigo, Spain
| | - Armando Caballero
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310, Vigo, Spain
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4
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Novo I, Pérez-Pereira N, Santiago E, Quesada H, Caballero A. An empirical test of the estimation of historical effective population size using Drosophila melanogaster. Mol Ecol Resour 2023; 23:1632-1640. [PMID: 37455584 DOI: 10.1111/1755-0998.13837] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/07/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
The availability of a large number of high-density markers (SNPs) allows the estimation of historical effective population size (Ne ) from linkage disequilibrium between loci. A recent refinement of methods to estimate historical Ne from the recent past has been shown to be rather accurate with simulation data. The method has also been applied to real data for numerous species. However, the simulation data cannot encompass all the complexities of real genomes, and the performance of any estimation method with real data is always uncertain, as the true demography of the populations is not known. Here, we carried out an experimental design with Drosophila melanogaster to test the method with real data following a known demographic history. We used a population maintained in the laboratory with a constant census size of about 2800 individuals and subjected the population to a drastic decline to a size of 100 individuals. After a few generations, the population was expanded back to the previous size and after a few further generations again expanded to twice the initial size. Estimates of historical Ne were obtained with the software GONE both for autosomal and X chromosomes from samples of 17 individuals sequenced for the whole genome. Estimates of the historical effective size were able to infer the patterns of changes that occurred in the populations showing generally good performance of the method. We discuss the limitations of the method and the application of the software carried out so far.
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Affiliation(s)
- Irene Novo
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Noelia Pérez-Pereira
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Enrique Santiago
- Departamento de Biología Funcional, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain
| | - Humberto Quesada
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Armando Caballero
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
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Platero F, Todorova S, Aoudjera L, Michelin L, Lebeau B, Blin JL, Holgado JP, Caballero A, Colón G. Cobalt Stabilization through Mesopore Confinement on TiO 2 Support for Fischer-Tropsch Reaction. ACS Appl Energy Mater 2023; 6:9475-9486. [PMID: 37771503 PMCID: PMC10523356 DOI: 10.1021/acsaem.3c01432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/29/2023] [Indexed: 09/30/2023]
Abstract
Cobalt supported on mesostructured TiO2 catalysts has been prepared by a wet-impregnation method. The Co/TiO2 catalytic system showed better catalytic performance after support calcination at 380 °C. Co nanoparticles appeared well distributed along the mesopore channels of TiO2. After reduction pretreatment and reaction, a drastic structural change leads to mesopore structure collapse and the dispersion of the Co nanoparticles on the external surface. Along this complex process, Co species first form discrete nanoparticles inside the pore and then diffuse out as the pore collapses. Through this confinement, a strong metal-support interaction effect is hindered, and highly stable metal active sites lead to better performance for Fischer-Tropsch synthesis reaction toward C5+ products.
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Affiliation(s)
- F. Platero
- Instituto
de Ciencia de Materiales de Sevilla, Centro Mixto Universidad de Sevilla-CSIC, Américo Vespucio, 49, 41092 Sevilla, Spain
| | - S. Todorova
- Institute
of Catalysis, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - L. Aoudjera
- Université
de Lorraine/CNRS, L2CM,
UMR7053, 54500 Vandoeuvre-lès-Nancy, France
| | - L. Michelin
- Université
de Haute Alsace, CNRS,
IS2M UMR 7361, 68100 Mulhouse, France
- Université
de Strasbourg, 67000 Strasbourg, France
| | - B. Lebeau
- Université
de Haute Alsace, CNRS,
IS2M UMR 7361, 68100 Mulhouse, France
- Université
de Strasbourg, 67000 Strasbourg, France
| | - J. L. Blin
- Université
de Lorraine/CNRS, L2CM,
UMR7053, 54500 Vandoeuvre-lès-Nancy, France
| | - J. P. Holgado
- Instituto
de Ciencia de Materiales de Sevilla, Centro Mixto Universidad de Sevilla-CSIC, Américo Vespucio, 49, 41092 Sevilla, Spain
| | - A. Caballero
- Instituto
de Ciencia de Materiales de Sevilla, Centro Mixto Universidad de Sevilla-CSIC, Américo Vespucio, 49, 41092 Sevilla, Spain
| | - G. Colón
- Instituto
de Ciencia de Materiales de Sevilla, Centro Mixto Universidad de Sevilla-CSIC, Américo Vespucio, 49, 41092 Sevilla, Spain
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Pérez‐Pereira N, Quesada H, Caballero A. An empirical evaluation of the estimation of inbreeding depression from molecular markers under suboptimal conditions. Evol Appl 2023; 16:1302-1315. [PMID: 37492144 PMCID: PMC10363801 DOI: 10.1111/eva.13568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 07/27/2023] Open
Abstract
Inbreeding depression (ID), the reduction in fitness due to inbreeding, is typically measured by the regression of the phenotypic values of individuals for a particular trait on their corresponding inbreeding coefficients (F). While genealogical records can provide these coefficients, they may be unavailable or incomplete, making molecular markers a useful alternative. The power to detect ID and its accuracy depend on the variation of F values of individuals, the sample sizes available, and the accuracy in the estimation of individual fitness traits and F values. In this study, we used Drosophila melanogaster to evaluate the effectiveness of molecular markers in estimating ID under suboptimal conditions. We generated two sets of 100 pairs of unrelated individuals from a large panmictic population and mated them for two generations to produce non-inbred and unrelated individuals (F = 0) and inbred individuals (full-sib progeny; F = 0.25). Using these expected genealogical F values, we calculated inbreeding depression for two fitness-related traits, pupae productivity and competitive fitness. We then sequenced the males from 17 non-inbred pairs and 17 inbred pairs to obtain their genomic inbreeding coefficients and estimate ID for the two traits. The scenario assumed was rather restrictive in terms of estimation of ID because: (1) the individuals belonged to the same generation of a large panmictic population, leading to low variation in individual F coefficients; (2) the sample sizes were small; and (3) the traits measured depended on both males and females while only males were sequenced. Despite the challenging conditions of our study, we found that molecular markers provided estimates of ID that were comparable to those obtained from simple pedigree estimations with larger sample sizes. The results therefore suggest that genomic measures of inbreeding are useful to provide estimates of inbreeding depression even under very challenging scenarios.
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Affiliation(s)
- Noelia Pérez‐Pereira
- Centro de Investigación MariñaUniversidade de Vigo, Facultade de BioloxíaVigoSpain
| | - Humberto Quesada
- Centro de Investigación MariñaUniversidade de Vigo, Facultade de BioloxíaVigoSpain
| | - Armando Caballero
- Centro de Investigación MariñaUniversidade de Vigo, Facultade de BioloxíaVigoSpain
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7
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Jin Y, Yasir S, Razzaq F, Calzada A, Virues T, Caballero A, Rodriguez-Labrada R, Bringas-Vega M, Valdes-Sosa P. qEEG mediates the effect of infection severity on COVID-induced brain dysfunction. Int J Psychophysiol 2023; 188:46-47. [PMCID: PMC10257129 DOI: 10.1016/j.ijpsycho.2023.05.118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
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8
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Coimbra MRM, Farias RDS, da Silva BC, Blanco A, Hermida M, Caballero A, Bekaert M, Martinez P. A genetic linkage map of the threatened catfish Lophiosilurus alexandri: Inferences on effective population size. Aquaculture and Fisheries 2023. [DOI: 10.1016/j.aaf.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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9
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Caballero A, Fernández A, Villanueva B, Toro MA. A comparison of marker-based estimators of inbreeding and inbreeding depression. Genet Sel Evol 2022; 54:82. [PMID: 36575379 PMCID: PMC9793638 DOI: 10.1186/s12711-022-00772-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The availability of genome-wide marker data allows estimation of inbreeding coefficients (F, the probability of identity-by-descent, IBD) and, in turn, estimation of the rate of inbreeding depression (ΔID). We investigated, by computer simulations, the accuracy of the most popular estimators of inbreeding based on molecular markers when computing F and ΔID in populations under random mating, equalization of parental contributions, and artificially selected populations. We assessed estimators described by Li and Horvitz (FLH1 and FLH2), VanRaden (FVR1 and FVR2), Yang and colleagues (FYA1 and FYA2), marker homozygosity (FHOM), runs of homozygosity (FROH) and estimates based on pedigree (FPED) in comparison with estimates obtained from IBD measures (FIBD). RESULTS If the allele frequencies of a base population taken as a reference for the computation of inbreeding are known, all estimators based on marker allele frequencies are highly correlated with FIBD and provide accurate estimates of the mean ΔID. If base population allele frequencies are unknown and current frequencies are used in the estimations, the largest correlation with FIBD is generally obtained by FLH1 and the best estimator of ΔID is FYA2. The estimators FVR2 and FLH2 have the poorest performance in most scenarios. The assumption that base population allele frequencies are equal to 0.5 results in very biased estimates of the average inbreeding coefficient but they are highly correlated with FIBD and give relatively good estimates of ΔID. Estimates obtained directly from marker homozygosity (FHOM) substantially overestimated ΔID. Estimates based on runs of homozygosity (FROH) provide accurate estimates of inbreeding and ΔID. Finally, estimates based on pedigree (FPED) show a lower correlation with FIBD than molecular estimators but provide rather accurate estimates of ΔID. An analysis of data from a pig population supports the main findings of the simulations. CONCLUSIONS When base population allele frequencies are known, all marker-allele frequency-based estimators of inbreeding coefficients generally show a high correlation with FIBD and provide good estimates of ΔID. When base population allele frequencies are unknown, FLH1 is the marker frequency-based estimator that is most correlated with FIBD, and FYA2 provides the most accurate estimates of ΔID. Estimates from FROH are also very precise in most scenarios. The estimators FVR2 and FLH2 have the poorest performances.
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Affiliation(s)
- Armando Caballero
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310 Vigo, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, INIA-CSIC, Ctra. de La Coruña, Km 7.5, 28040 Madrid, Spain
| | - Beatriz Villanueva
- Departamento de Mejora Genética Animal, INIA-CSIC, Ctra. de La Coruña, Km 7.5, 28040 Madrid, Spain
| | - Miguel A. Toro
- grid.5690.a0000 0001 2151 2978Departamento de Producción Agraria, ETSI Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
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Ramos-Zaldívar H, Reyes-Perdomo K, Espinoza-Moreno N, Dox-Cruz E, Urbina T, Caballero A, Dominguez E, Calix S, Monterroso-Reyes J, Vásquez E, Ortiz T, Rodríguez-Machado H, Solis M, Silva I, Galeano M, Alvarado A, Medina A, Guerrero-Díaz L, Jiménez-Faraj J, Santos C, Arita W, Montufar D, Sabillón J, Sorto M, Navarro X, Palomo-Bermúdez V, Andino H, Guzman S, Reyes M, Pazf E, Enamorado J, Sagastume Y, Rivera A, Sarmiento C, Pineda X, Puerto V, Landaverde J, Reyes S, Perdomo I, Rivera J, Girón W, Sabillón K, Leiva P, Toro K, Montes-Gambarelli J, Flores C, Salas-Huenuleo E, Andia M. SAFETY AND EFFICACY OF THYMIC PEPTIDES IN THE TREATMENT OF HOSPITALIZED COVID-19 PATIENTS IN HONDURAS. Georgian Med News 2022:99-105. [PMID: 36427851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Coronavirus disease 2019 (Covid-19) active cases continue to demand the development of safe and effective treatments. This is the first clinical trial to evaluate the safety and efficacy of oral thymic peptides. ; We conducted a nonrandomized phase 2 trial with a historic control group to evaluate the safety and efficacy of a daily 250-mg oral dose of thymic peptides in the treatment of hospitalized Covid-19 patients. Comparisons based on standard care from registry data were performed after propensity score matching. The primary outcomes were survival, time to recovery, and number of participants with treatment-related adverse events or side effects by day 20. ; A total of 44 patients were analyzed in this study: 22 in the thymic peptide group and 22 in the standard care group. There were no deaths in the intervention group compared to 24% mortality in standard care by day 20 (log-rank P=0.02). Kaplan-Meier analysis showed a significantly shorter time to recovery by day 20 in the thymic peptide group than in the standard care group (median, 6 days vs. 12 days; hazard ratio for recovery, 2.75 [95% confidence interval, 1.34 to 5.62]; log-rank P=0.002). No side effects or adverse events were reported. ; In patients hospitalized with Covid-19, the use of thymic peptides resulted in no side effects, adverse events, or deaths by day 20. Compared with the registry data, a significantly shorter time to recovery and mortality reduction were measured.
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Affiliation(s)
- H Ramos-Zaldívar
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras; 2Doctoral Program in Medical Sciences, Faculty of Medicine, Pontificia Universidad Católica de Chile
| | - K Reyes-Perdomo
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras; 3Psiquiatría Infantil y del Adolescente, Hospital Barros Luco Trudeau, Facultad de Ciencias Médicas, Universidad de Santiago de Chile
| | - N Espinoza-Moreno
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - E Dox-Cruz
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - Th Urbina
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - A Caballero
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - E Dominguez
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - S Calix
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - J Monterroso-Reyes
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - E Vásquez
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - T Ortiz
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - H Rodríguez-Machado
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - M Solis
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - I Silva
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - M Galeano
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - A Alvarado
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - A Medina
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - L Guerrero-Díaz
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - J Jiménez-Faraj
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras; 4Hospital Civil de Guadalajara Juan I. Menchaca, México
| | - C Santos
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras; 5Hospital del Valle, San Pedro Sula, Honduras
| | - W Arita
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - D Montufar
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - J Sabillón
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - M Sorto
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - X Navarro
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - V Palomo-Bermúdez
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras; 5Hospital del Valle, San Pedro Sula, Honduras
| | - H Andino
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - S Guzman
- 6Hospital Santa Bárbara Integrado, Santa Bárbara, Honduras
| | - M Reyes
- 6Hospital Santa Bárbara Integrado, Santa Bárbara, Honduras
| | - E Pazf
- 6Hospital Santa Bárbara Integrado, Santa Bárbara, Honduras
| | - J Enamorado
- 6Hospital Santa Bárbara Integrado, Santa Bárbara, Honduras
| | - Y Sagastume
- 6Hospital Santa Bárbara Integrado, Santa Bárbara, Honduras
| | - A Rivera
- 6Hospital Santa Bárbara Integrado, Santa Bárbara, Honduras
| | - C Sarmiento
- 6Hospital Santa Bárbara Integrado, Santa Bárbara, Honduras
| | - X Pineda
- 6Hospital Santa Bárbara Integrado, Santa Bárbara, Honduras
| | - V Puerto
- 6Hospital Santa Bárbara Integrado, Santa Bárbara, Honduras
| | - J Landaverde
- 6Hospital Santa Bárbara Integrado, Santa Bárbara, Honduras6Hospital Santa Bárbara Integrado, Santa Bárbara, Honduras
| | - S Reyes
- 6Hospital Santa Bárbara Integrado, Santa Bárbara, Honduras
| | - I Perdomo
- 6Hospital Santa Bárbara Integrado, Santa Bárbara, Honduras
| | - J Rivera
- 6Hospital Santa Bárbara Integrado, Santa Bárbara, Honduras
| | - W Girón
- 6Hospital Santa Bárbara Integrado, Santa Bárbara, Honduras
| | - K Sabillón
- 6Hospital Santa Bárbara Integrado, Santa Bárbara, Honduras
| | - P Leiva
- 7Triaje de Santa Bárbara, Secretaría de Salud de Honduras
| | - K Toro
- 7Triaje de Santa Bárbara, Secretaría de Salud de Honduras
| | - J Montes-Gambarelli
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras
| | - C Flores
- 1Grupo de Investigación Médica de la Universidad Católica de Honduras, (GIMUNICAH), Faculty of Medicine, Universidad Católica de Honduras; 8Laboratorio de Biología Molecular de San Pedro Sula, Secretaría de Salud de Honduras
| | | | - M Andia
- 10Biomedical Imaging Center Radiology Department, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile; 11Millennium Nucleus in Cardiovascular Magnetic Resonance, Santiago, Chile
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11
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Pérez‐Pereira N, López‐Cortegano E, García‐Dorado A, Caballero A. Prediction of fitness under different breeding designs in conservation programs. Anim Conserv 2022. [DOI: 10.1111/acv.12804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- N. Pérez‐Pereira
- Centro de Investigación Mariña Universidade de Vigo, Facultade de Bioloxía Vigo Spain
| | - E. López‐Cortegano
- Centro de Investigación Mariña Universidade de Vigo, Facultade de Bioloxía Vigo Spain
| | - A. García‐Dorado
- Departamento de Genética, Facultad de Ciencias Biológicas Universidad Complutense Madrid Spain
| | - A. Caballero
- Centro de Investigación Mariña Universidade de Vigo, Facultade de Bioloxía Vigo Spain
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12
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Novo I, Santiago E, Caballero A. The estimates of effective population size based on linkage disequilibrium are virtually unaffected by natural selection. PLoS Genet 2022; 18:e1009764. [PMID: 35077457 PMCID: PMC8815936 DOI: 10.1371/journal.pgen.1009764] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 02/04/2022] [Accepted: 12/21/2021] [Indexed: 11/19/2022] Open
Abstract
The effective population size (Ne) is a key parameter to quantify the magnitude of genetic drift and inbreeding, with important implications in human evolution. The increasing availability of high-density genetic markers allows the estimation of historical changes in Ne across time using measures of genome diversity or linkage disequilibrium between markers. Directional selection is expected to reduce diversity and Ne, and this reduction is modulated by the heterogeneity of the genome in terms of recombination rate. Here we investigate by computer simulations the consequences of selection (both positive and negative) and recombination rate heterogeneity in the estimation of historical Ne. We also investigate the relationship between diversity parameters and Ne across the different regions of the genome using human marker data. We show that the estimates of historical Ne obtained from linkage disequilibrium between markers (NeLD) are virtually unaffected by selection. In contrast, those estimates obtained by coalescence mutation-recombination-based methods can be strongly affected by it, which could have important consequences for the estimation of human demography. The simulation results are supported by the analysis of human data. The estimates of NeLD obtained for particular genomic regions do not correlate, or they do it very weakly, with recombination rate, nucleotide diversity, proportion of polymorphic sites, background selection statistic, minor allele frequency of SNPs, loss of function and missense variants and gene density. This suggests that NeLD measures mainly reflect demographic changes in population size across generations. The inference of the demographic history of populations is of great relevance in evolutionary biology. This inference can be made from genomic data using coalescence methods or linkage disequilibrium methods. However, the assessment of these methods is usually made assuming neutrality (absence of selection). Here we show by computer simulations and analyses of human data that the estimates of historical effective population size obtained from linkage disequilibrium between markers are virtually unaffected by natural selection, either positive or negative. In contrast, estimates obtained by coalescence mutation-recombination-based methods can be strongly affected by it, which could have important consequences for recent estimations of human demography.
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Affiliation(s)
- Irene Novo
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
- * E-mail:
| | - Enrique Santiago
- Departamento de Biología Funcional, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain
| | - Armando Caballero
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
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13
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Saura M, Caballero A, Santiago E, Fernández A, Morales-González E, Fernández J, Cabaleiro S, Millán A, Martínez P, Palaiokostas C, Kocour M, Aslam ML, Houston RD, Prchal M, Bargelloni L, Tzokas K, Haffray P, Bruant JS, Villanueva B. Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes. Genet Sel Evol 2021; 53:85. [PMID: 34742227 PMCID: PMC8572424 DOI: 10.1186/s12711-021-00680-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 10/22/2021] [Indexed: 11/15/2022] Open
Abstract
Background The high fecundity of fish species allows intense selection to be practised and therefore leads to fast genetic gains. Based on this, numerous selective breeding programmes have been started in Europe in the last decades, but in general, little is known about how the base populations of breeders have been built. Such knowledge is important because base populations can be created from very few individuals, which can lead to small effective population sizes and associated reductions in genetic variability. In this study, we used genomic information that was recently made available for turbot (Scophthalmus maximus), gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax) and common carp (Cyprinus carpio) to obtain accurate estimates of the effective size for commercial populations. Methods Restriction-site associated DNA sequencing data were used to estimate current and historical effective population sizes. We used a novel method that considers the linkage disequilibrium spectrum for the whole range of genetic distances between all pairs of single nucleotide polymorphisms (SNPs), and thus accounts for potential fluctuations in population size over time. Results Our results show that the current effective population size for these populations is small (equal to or less than 50 fish), potentially putting the sustainability of the breeding programmes at risk. We have also detected important drops in effective population size about five to nine generations ago, most likely as a result of domestication and the start of selective breeding programmes for these species in Europe. Conclusions Our findings highlight the need to broaden the genetic composition of the base populations from which selection programmes start, and suggest that measures designed to increase effective population size within all farmed populations analysed here should be implemented in order to manage genetic variability and ensure the sustainability of the breeding programmes. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00680-9.
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Affiliation(s)
- María Saura
- Departamento de Mejora Genética Animal, INIA-CSIC, Ctra. de La Coruña, km 7.5, 28040, Madrid, Spain.
| | - Armando Caballero
- Centro de Investigación Mariña, Facultade de Bioloxía, Universidade de Vigo, 36310, Vigo, Spain
| | - Enrique Santiago
- Departamento de Biología Funcional, Universidad de Oviedo, C/ Julián Clavería s/n, 33006, Oviedo, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, INIA-CSIC, Ctra. de La Coruña, km 7.5, 28040, Madrid, Spain
| | | | - Jesús Fernández
- Departamento de Mejora Genética Animal, INIA-CSIC, Ctra. de La Coruña, km 7.5, 28040, Madrid, Spain
| | - Santiago Cabaleiro
- CETGA, Cluster de Acuicultura de Galicia, Punta do Couso s/n, 15695, Aguiño-Ribeira, Spain
| | | | - Paulino Martínez
- Departament of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, 27002, Lugo, Spain
| | - Christos Palaiokostas
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Martin Kocour
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25, Vodňany, Czech Republic
| | | | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Martin Prchal
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25, Vodňany, Czech Republic
| | - Luca Bargelloni
- Universitá degli Studi di Padova, Via 8 Febbraio 1848, 2, 35122, Padova, PD, Italy
| | - Kostas Tzokas
- Andromeda Group SA, Leof. Lavriou 99, 190 02, Peania, Greece
| | - Pierrick Haffray
- SYSAAF, Station LPGP/INRAE, Campus de Beaulieu, 35042, Rennes, France
| | | | - Beatriz Villanueva
- Departamento de Mejora Genética Animal, INIA-CSIC, Ctra. de La Coruña, km 7.5, 28040, Madrid, Spain
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14
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Pérez-Pereira N, Pouso R, Rus A, Vilas A, López-Cortegano E, García-Dorado A, Quesada H, Caballero A. Long-term exhaustion of the inbreeding load in Drosophila melanogaster. Heredity (Edinb) 2021; 127:373-383. [PMID: 34400819 PMCID: PMC8478893 DOI: 10.1038/s41437-021-00464-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 07/29/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
Inbreeding depression, the decline in fitness of inbred individuals, is a ubiquitous phenomenon of great relevance in evolutionary biology and in the fields of animal and plant breeding and conservation. Inbreeding depression is due to the expression of recessive deleterious alleles that are concealed in heterozygous state in noninbred individuals, the so-called inbreeding load. Genetic purging reduces inbreeding depression by removing these alleles when expressed in homozygosis due to inbreeding. It is generally thought that fast inbreeding (such as that generated by full-sib mating lines) removes only highly deleterious recessive alleles, while slow inbreeding can also remove mildly deleterious ones. However, a question remains regarding which proportion of the inbreeding load can be removed by purging under slow inbreeding in moderately large populations. We report results of two long-term slow inbreeding Drosophila experiments (125-234 generations), each using a large population and a number of derived lines with effective sizes about 1000 and 50, respectively. The inbreeding load was virtually exhausted after more than one hundred generations in large populations and between a few tens and over one hundred generations in the lines. This result is not expected from genetic drift alone, and is in agreement with the theoretical purging predictions. Computer simulations suggest that these results are consistent with a model of relatively few deleterious mutations of large homozygous effects and partially recessive gene action.
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Affiliation(s)
- Noelia Pérez-Pereira
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Ramón Pouso
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Ana Rus
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Ana Vilas
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Eugenio López-Cortegano
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain ,grid.4305.20000 0004 1936 7988Present Address: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Aurora García-Dorado
- grid.4795.f0000 0001 2157 7667Facultad de Ciencias Biológicas, Departamento de Genética, Universidad Complutense, Madrid, Spain
| | - Humberto Quesada
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Armando Caballero
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
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15
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Novo I, López-Cortegano E, Caballero A. Highly pleiotropic variants of human traits are enriched in genomic regions with strong background selection. Hum Genet 2021; 140:1343-1351. [PMID: 34228221 PMCID: PMC8338839 DOI: 10.1007/s00439-021-02308-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/18/2021] [Indexed: 11/27/2022]
Abstract
Recent studies have shown the ubiquity of pleiotropy for variants affecting human complex traits. These studies also show that rare variants tend to be less pleiotropic than common ones, suggesting that purifying natural selection acts against highly pleiotropic variants of large effect. Here, we investigate the mean frequency, effect size and recombination rate associated with pleiotropic variants, and focus particularly on whether highly pleiotropic variants are enriched in regions with putative strong background selection. We evaluate variants for 41 human traits using data from the NHGRI-EBI GWAS Catalog, as well as data from other three studies. Our results show that variants involving a higher degree of pleiotropy tend to be more common, have larger mean effect sizes, and contribute more to heritability than variants with a lower degree of pleiotropy. This is consistent with the fact that variants of large effect and frequency are more likely detected by GWAS. Using data from four different studies, we also show that more pleiotropic variants are enriched in genome regions with stronger background selection than less pleiotropic variants, suggesting that highly pleiotropic variants are subjected to strong purifying selection. From the above results, we hypothesized that a number of highly pleiotropic variants of low effect/frequency may pass undetected by GWAS.
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Affiliation(s)
- Irene Novo
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310, Vigo, Spain.
| | - Eugenio López-Cortegano
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310, Vigo, Spain
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Armando Caballero
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310, Vigo, Spain
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16
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17
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Villanueva B, Fernández A, Saura M, Caballero A, Fernández J, Morales-González E, Toro MA, Pong-Wong R. The value of genomic relationship matrices to estimate levels of inbreeding. Genet Sel Evol 2021; 53:42. [PMID: 33933002 PMCID: PMC8088726 DOI: 10.1186/s12711-021-00635-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 04/19/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Genomic relationship matrices are used to obtain genomic inbreeding coefficients. However, there are several methodologies to compute these matrices and there is still an unresolved debate on which one provides the best estimate of inbreeding. In this study, we investigated measures of inbreeding obtained from five genomic matrices, including the Nejati-Javaremi allelic relationship matrix (FNEJ), the Li and Horvitz matrix based on excess of homozygosity (FL&H), and the VanRaden (methods 1, FVR1, and 2, FVR2) and Yang (FYAN) genomic relationship matrices. We derived expectations for each inbreeding coefficient, assuming a single locus model, and used these expectations to explain the patterns of the coefficients that were computed from thousands of single nucleotide polymorphism genotypes in a population of Iberian pigs. RESULTS Except for FNEJ, the evaluated measures of inbreeding do not match with the original definitions of inbreeding coefficient of Wright (correlation) or Malécot (probability). When inbreeding coefficients are interpreted as indicators of variability (heterozygosity) that was gained or lost relative to a base population, both FNEJ and FL&H led to sensible results but this was not the case for FVR1, FVR2 and FYAN. When variability has increased relative to the base, FVR1, FVR2 and FYAN can indicate that it decreased. In fact, based on FYAN, variability is not expected to increase. When variability has decreased, FVR1 and FVR2 can indicate that it has increased. Finally, these three coefficients can indicate that more variability than that present in the base population can be lost, which is also unreasonable. The patterns for these coefficients observed in the pig population were very different, following the derived expectations. As a consequence, the rate of inbreeding depression estimated based on these inbreeding coefficients differed not only in magnitude but also in sign. CONCLUSIONS Genomic inbreeding coefficients obtained from the diagonal elements of genomic matrices can lead to inconsistent results in terms of gain and loss of genetic variability and inbreeding depression estimates, and thus to misleading interpretations. Although these matrices have proven to be very efficient in increasing the accuracy of genomic predictions, they do not always provide a useful measure of inbreeding.
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Affiliation(s)
- Beatriz Villanueva
- Departamento de Mejora Genética Animal, INIA, Ctra. de La Coruña, km 7.5, 28040 Madrid, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, INIA, Ctra. de La Coruña, km 7.5, 28040 Madrid, Spain
| | - María Saura
- Departamento de Mejora Genética Animal, INIA, Ctra. de La Coruña, km 7.5, 28040 Madrid, Spain
| | - Armando Caballero
- Centro de Investigación Mariña, Universidade de Vigo, Departamento de Bioquímica, Genética E Inmunología, Campus de Vigo, 36310 Vigo, Spain
| | - Jesús Fernández
- Departamento de Mejora Genética Animal, INIA, Ctra. de La Coruña, km 7.5, 28040 Madrid, Spain
| | | | - Miguel A. Toro
- Departamento de Producción Agraria, ETSI Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Ricardo Pong-Wong
- Genetics and Genomics, The Roslin Institute and the R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
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18
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Agudelo-Arrieta M, Vergara-Garcia D, Madrinan-Navia H, Palmera-Pineda H, Vergara-Dagobeth E, Riveros WM, Caballero A. Concurrent carotid-cavernous fistula and cervical internal carotid artery pseudoaneurysm due to a gunshot injury: A case report. Neurochirurgie 2021; 68:133-136. [PMID: 33771618 DOI: 10.1016/j.neuchi.2021.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/17/2021] [Accepted: 03/06/2021] [Indexed: 10/21/2022]
Affiliation(s)
- M Agudelo-Arrieta
- Department of Neurosurgery, Center for Research and Training in Neurosurgery (CIEN), Samaritana University Hospital, Rosario University School of Medicine, Bogotá, Colombia
| | - D Vergara-Garcia
- Department of Neurosurgery, Center for Research and Training in Neurosurgery (CIEN), Samaritana University Hospital, Rosario University School of Medicine, Bogotá, Colombia.
| | - H Madrinan-Navia
- Department of Neurosurgery, Center for Research and Training in Neurosurgery (CIEN), Samaritana University Hospital, Rosario University School of Medicine, Bogotá, Colombia
| | - H Palmera-Pineda
- Department of Neurosurgery, Central Military Hospital, Nueva Granada Military University, Bogotá, Colombia
| | - E Vergara-Dagobeth
- Department of Surgery, Sucre University School of Medicine, Sincelejo, Colombia
| | - W M Riveros
- Department of Neurosurgery, Center for Research and Training in Neurosurgery (CIEN), Samaritana University Hospital, Rosario University School of Medicine, Bogotá, Colombia
| | - A Caballero
- Department of Neurosurgery, Center for Research and Training in Neurosurgery (CIEN), Samaritana University Hospital, Rosario University School of Medicine, Bogotá, Colombia; Department of Neurosurgery, Central Military Hospital, Nueva Granada Military University, Bogotá, Colombia
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19
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Caballero A, Villanueva B, Druet T. On the estimation of inbreeding depression using different measures of inbreeding from molecular markers. Evol Appl 2021; 14:416-428. [PMID: 33664785 PMCID: PMC7896712 DOI: 10.1111/eva.13126] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 07/09/2020] [Accepted: 08/26/2020] [Indexed: 12/20/2022] Open
Abstract
The inbreeding coefficient (F) of individuals can be estimated from molecular marker data, such as SNPs, using measures of homozygosity of individual markers or runs of homozygosity (ROH) across the genome. These different measures of F can then be used to estimate the rate of inbreeding depression (ID) for quantitative traits. Some recent simulation studies have investigated the accuracy of this estimation with contradictory results. Whereas some studies suggest that estimates of inbreeding from ROH account more accurately for ID, others suggest that inbreeding measures from SNP-by-SNP homozygosity giving a large weight to rare alleles are more accurate. Here, we try to give more light on this issue by carrying out a set of computer simulations considering a range of population genetic parameters and population sizes. Our results show that the previous studies are indeed not contradictory. In populations with low effective size, where relationships are more tight and selection is relatively less intense, F measures based on ROH provide very accurate estimates of ID whereas SNP-by-SNP-based F measures with high weight to rare alleles can show substantial upwardly biased estimates of ID. However, in populations of large effective size, with more intense selection and trait allele frequencies expected to be low if they are deleterious for fitness because of purifying selection, average estimates of ID from SNP-by-SNP-based F values become unbiased or slightly downwardly biased and those from ROH-based F values become slightly downwardly biased. The noise attached to all these estimates, nevertheless, can be very high in large-sized populations. We also investigate the relationship between the different F measures and the homozygous mutation load, which has been suggested as a proxy of inbreeding depression.
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Affiliation(s)
- Armando Caballero
- Centro de Investigación Mariña, Departamento de Bioquímica, Genética e Inmunología, Edificio CC ExperimentaisUniversidade de VigoVigoSpain
| | - Beatriz Villanueva
- Departamento de Mejora GenéticaInstituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadridSpain
| | - Tom Druet
- Unit of Animal GenomicsGIGA‐R & Faculty of Veterinary MedicineUniversity of LiègeLiègeBelgium
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20
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Filgueira LM, Cervantes JB, Lovelle OA, Herrera C, Figueredo C, Caballero JA, Sánchez N, Berrio J, Lorenzo G, Cepeda M, Ramos M, Saavedra D, Añe-Kouri AL, Mazorra Z, Leon K, Crombet T, Caballero A. An anti-CD6 antibody for the treatment of COVID-19 patients with cytokine-release syndrome: report of three cases. Immunotherapy 2021; 13:289-295. [PMID: 33397150 PMCID: PMC7784786 DOI: 10.2217/imt-2020-0235] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In COVID-19, the inflammatory cytokine-release syndrome is associated with the progression of the disease. Itolizumab is a monoclonal antibody that recognizes human CD6 expressed in activated T cells. The antibody has shown to be safe and efficacious in the treatment of moderate to severe psoriasis. Its effect is associated with the reduction of pro-inflammatory cytokines release, including IFN-γ, IL-6 and TNF-α. Here, we report the outcome of three severe and critically ill COVID-19 patients treated with itolizumab as part of an expanded access protocol. Itolizumab was able to reduce IL-6 concentrations in all the patients. Two of the three patients showed respiratory and radiological improvement and were fully recovered. We hypothesize this anti-inflammatory therapy in addition to antiviral and anticoagulant therapy could reduce COVID-19 associated morbidity and mortality.
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Affiliation(s)
- Lázaro Manuel Filgueira
- Manuel Piti Fajardo University Hospital, Ciudad Escolar Abel Santamaría. U/M 9958, Santa Clara city, Villa Clara, Cuba
| | - Julio Betancourt Cervantes
- Manuel Piti Fajardo University Hospital, Ciudad Escolar Abel Santamaría. U/M 9958, Santa Clara city, Villa Clara, Cuba
| | - Orlando Adolfo Lovelle
- Manuel Piti Fajardo University Hospital, Ciudad Escolar Abel Santamaría. U/M 9958, Santa Clara city, Villa Clara, Cuba
| | - Carlos Herrera
- Arnaldo Milián University Hospital, Santa Clara St., Santa Clara city, Villa Clara, Cuba
| | - Carlos Figueredo
- Manuel Piti Fajardo University Hospital, Ciudad Escolar Abel Santamaría. U/M 9958, Santa Clara city, Villa Clara, Cuba
| | - Jorge Alain Caballero
- Arnaldo Milián University Hospital, Santa Clara St., Santa Clara city, Villa Clara, Cuba
| | - Naivy Sánchez
- Manuel Piti Fajardo University Hospital, Ciudad Escolar Abel Santamaría. U/M 9958, Santa Clara city, Villa Clara, Cuba
| | - Jorge Berrio
- Manuel Piti Fajardo University Hospital, Ciudad Escolar Abel Santamaría. U/M 9958, Santa Clara city, Villa Clara, Cuba
| | - Geidy Lorenzo
- Center of Molecular Immunology, 216 St, corner 15, Atabey, Havana, Cuba
| | - Meylan Cepeda
- Center of Molecular Immunology, 216 St, corner 15, Atabey, Havana, Cuba
| | - Mayra Ramos
- Center of Molecular Immunology, 216 St, corner 15, Atabey, Havana, Cuba
| | - Danay Saavedra
- Center of Molecular Immunology, 216 St, corner 15, Atabey, Havana, Cuba
| | - Ana Laura Añe-Kouri
- Superior Institute of Basic & Preclinical Sciences of Havana "Victoria de Girón", Street 25, Playa, Havana, Cuba
| | - Zaima Mazorra
- Center of Molecular Immunology, 216 St, corner 15, Atabey, Havana, Cuba
| | - Kalet Leon
- Center of Molecular Immunology, 216 St, corner 15, Atabey, Havana, Cuba
| | - Tania Crombet
- Center of Molecular Immunology, 216 St, corner 15, Atabey, Havana, Cuba
| | - Armando Caballero
- Arnaldo Milián University Hospital, Santa Clara St., Santa Clara city, Villa Clara, Cuba
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Caballero A, Filgueira LM, Betancourt J, Sánchez N, Hidalgo C, Ramírez A, Martinez A, Despaigne RE, Escalona A, Diaz H, Meriño E, Ortega LM, Castillo U, Ramos M, Saavedra D, García Y, Lorenzo G, Cepeda M, Arencibia M, Cabrera L, Domecq M, Estévez D, Valenzuela C, Lorenzo P, Sánchez L, Mazorra Z, León K, Crombet T. Treatment of COVID-19 patients with the anti-CD6 antibody itolizumab. Clin Transl Immunology 2020; 9:e1218. [PMID: 33304584 PMCID: PMC7688906 DOI: 10.1002/cti2.1218] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/02/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022] Open
Abstract
Objectives COVID‐19 can lead to a hyperinflammatory state. CD6 is a glycoprotein expressed on mature T lymphocytes which is a crucial regulator of the T‐cell activation. Itolizumab is a humanised antibody targeting CD6. Nonclinical and clinical data in autoimmune diseases indicate that it lowers multiple cytokines primarily involving the Th1/Th17 pathway. The primary objective of this study was to assess the impact of itolizumab in arresting the lung function deterioration of COVID‐19 patients. Secondary objectives included safety, duration of ventilation, 14‐day mortality and evaluation of interleukin 6 concentration. Methods Patients with confirmed SARS‐CoV‐2 received itolizumab in combination with other therapies included in the national protocol for COVID‐19. Results Seventy critical, severe or moderate patients were treated with itolizumab in 10 Cuban hospitals. Median age was 68, and 94% had comorbidities. After 72 h, most patients improved the PO2/FiO2 ratio and reduced FiO2 requirements. Ventilation time was 8 days for critical and 1 day for severe cases. Ten patients had related adverse events while 3 subjects developed related serious events. In 30 patients, interleukin 6 decreased in individuals with high level and did not change in those with lower concentration. Fourteen‐day lethality rate was 4% and 18% for moderate and severe patients, respectively. The proportion of moderate or severe patients with ventilation or death at day 14 was 9.8%. Time to treatment, neurological manifestations and biomarkers such as NLR were significantly associated with higher lethality. Conclusions The opportune administration of itolizumab might interrupt the hyperinflammatory cascade and prevent COVID‐19 morbidity and mortality.
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Affiliation(s)
- Armando Caballero
- Intensive Care Unit Arnaldo Milián Castro University Hospital Santa Clara Cuba
| | - Lázaro M Filgueira
- Intensive Care Unit Manuel "Piti" Fajardo Rivero Hospital Santa Clara Cuba
| | - Julio Betancourt
- Intensive Care Unit Manuel "Piti" Fajardo Rivero Hospital Santa Clara Cuba
| | - Naivy Sánchez
- Intensive Care Unit Manuel "Piti" Fajardo Rivero Hospital Santa Clara Cuba
| | - Carlos Hidalgo
- Intensive Care Unit Manuel "Piti" Fajardo Rivero Hospital Santa Clara Cuba
| | | | | | | | | | - Henrry Diaz
- Intensive Care Unit Frank País Hospital Havana Cuba
| | - Elio Meriño
- Intensive Care Unit Frank País Hospital Havana Cuba
| | | | | | - Mayra Ramos
- Clinical Research Direction Center of Molecular Immunology (CIM) Havana Cuba
| | - Danay Saavedra
- Clinical Research Direction Center of Molecular Immunology (CIM) Havana Cuba
| | - Yanelda García
- Clinical Research Direction Center of Molecular Immunology (CIM) Havana Cuba
| | - Geydi Lorenzo
- Clinical Research Direction Center of Molecular Immunology (CIM) Havana Cuba
| | - Meylán Cepeda
- Clinical Research Direction Center of Molecular Immunology (CIM) Havana Cuba
| | - Maylén Arencibia
- Clinical Research Direction Center of Molecular Immunology (CIM) Havana Cuba
| | - Leticia Cabrera
- Clinical Research Direction Center of Molecular Immunology (CIM) Havana Cuba
| | - Milagros Domecq
- Clinical Research Direction Center of Molecular Immunology (CIM) Havana Cuba
| | - Daymys Estévez
- Clinical Research Direction Center of Molecular Immunology (CIM) Havana Cuba
| | - Carmen Valenzuela
- Clinical Research Direction Center of Molecular Immunology (CIM) Havana Cuba
| | - Patricia Lorenzo
- Clinical Research Direction Center of Molecular Immunology (CIM) Havana Cuba
| | - Lizet Sánchez
- Clinical Research Direction Center of Molecular Immunology (CIM) Havana Cuba
| | - Zaima Mazorra
- Clinical Research Direction Center of Molecular Immunology (CIM) Havana Cuba
| | - Kalet León
- Research Direction Center of Molecular Immunology (CIM) Havana Cuba
| | - Tania Crombet
- Clinical Research Direction Center of Molecular Immunology (CIM) Havana Cuba
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22
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Alemu SW, Kadri NK, Harland C, Faux P, Charlier C, Caballero A, Druet T. An evaluation of inbreeding measures using a whole-genome sequenced cattle pedigree. Heredity (Edinb) 2020; 126:410-423. [PMID: 33159183 PMCID: PMC8027009 DOI: 10.1038/s41437-020-00383-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 10/23/2020] [Accepted: 10/23/2020] [Indexed: 11/13/2022] Open
Abstract
The estimation of the inbreeding coefficient (F) is essential for the study of inbreeding depression (ID) or for the management of populations under conservation. Several methods have been proposed to estimate the realized F using genetic markers, but it remains unclear which one should be used. Here we used whole-genome sequence data for 245 individuals from a Holstein cattle pedigree to empirically evaluate which estimators best capture homozygosity at variants causing ID, such as rare deleterious alleles or loci presenting heterozygote advantage and segregating at intermediate frequency. Estimators relying on the correlation between uniting gametes (FUNI) or on the genomic relationships (FGRM) presented the highest correlations with these variants. However, homozygosity at rare alleles remained poorly captured. A second group of estimators relying on excess homozygosity (FHOM), homozygous-by-descent segments (FHBD), runs-of-homozygosity (FROH) or on the known genealogy (FPED) was better at capturing whole-genome homozygosity, reflecting the consequences of inbreeding on all variants, and for young alleles with low to moderate frequencies (0.10 < . < 0.25). The results indicate that FUNI and FGRM might present a stronger association with ID. However, the situation might be different when recessive deleterious alleles reach higher frequencies, such as in populations with a small effective population size. For locus-specific inbreeding measures or at low marker density, the ranking of the methods can also change as FHBD makes better use of the information from neighboring markers. Finally, we confirmed that genomic measures are in general superior to pedigree-based estimates. In particular, FPED was uncorrelated with locus-specific homozygosity.
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Affiliation(s)
- Setegn Worku Alemu
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Naveen Kumar Kadri
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Chad Harland
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Pierre Faux
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Carole Charlier
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Armando Caballero
- Centro de Investigación Mariña, Departamento de Bioquímica, Genética e Inmunología, Edificio CC Experimentais, Universidade de Vigo, Campus de Vigo, As Lagoas, Marcosende, 36310, Vigo, Spain
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
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Díaz Y, Ramos-Suzarte M, Martín Y, Calderón NA, Santiago W, Viñet O, La O Y, Oyarzábal JPA, Pérez Y, Lorenzo G, Cepeda M, Saavedra D, Mazorra Z, Estevez D, Lorenzo-Luaces P, Valenzuela C, Caballero A, Leon K, Crombet T, Hidalgo CJ. Use of a Humanized Anti-CD6 Monoclonal Antibody (Itolizumab) in Elderly Patients with Moderate COVID-19. Gerontology 2020; 66:553-561. [PMID: 33105142 PMCID: PMC7649683 DOI: 10.1159/000512210] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/10/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a recent outbreak of coronavirus disease (COVID-19). In Cuba, the first case of COVID-19 was reported on March 11, 2020. Elderly individuals with multiple comorbidities are particularly susceptible to adverse clinical outcomes in the course of SARS-CoV-2 infection. During the outbreak, a local transmission event took place in a nursing home in Villa Clara province, Cuba, in which 19 elderly residents tested positive for SARS-CoV-2. METHODS Based on the increased susceptibility to cytokine release syndrome, inducing respiratory and systemic complications in this population, 19 patients were included in an expanded access clinical trial to receive itolizumab, an anti-CD6 monoclonal antibody. RESULTS All patients had underlying medical conditions. The product was well tolerated. After the first dose, the course of the disease was favorable, and 18 of the 19 patients (94.7%) were discharged clinically recovered with negative real-time reverse transcription polymerase chain reaction test results at 13 days. After one dose of itolizumab, circulating IL-6 decreased within the first 24-48 h in patients with high baseline values, whereas in patients with low levels, this concentration remained over low values. To preliminarily assess the effect of itolizumab, a control group was selected among the Cuban COVID-19 patients that did not receive immunomodulatory therapy. The control subjects were well matched regarding age, comorbidities, and severity of the disease. The percentage of itolizumab-treated, moderately ill patients who needed to be admitted to the intensive care unit was only one-third of that of the control group not treated with itolizumab. Additionally, treatment with itolizumab reduced the risk of death 10 times as compared with the control group. CONCLUSION This study corroborates that the timely use of itolizumab in combination with other antivirals reduces COVID-19 disease worsening and mortality. The humanized antibody itolizumab emerges as a therapeutic alternative for patients with COVID-19. Our results suggest the possible use of itolizumab in patients with cytokine release syndrome from other pathologies.
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Affiliation(s)
- Yayquier Díaz
- Manuel Fajardo University Hospital, Santa Clara, Cuba
| | | | | | | | | | - Orlando Viñet
- Manuel Fajardo University Hospital, Santa Clara, Cuba
| | - Yulieski La O
- Manuel Fajardo University Hospital, Santa Clara, Cuba
| | | | - Yoan Pérez
- Manuel Fajardo University Hospital, Santa Clara, Cuba
| | | | | | | | | | | | | | | | | | - Kalet Leon
- Center of Molecular Immunology, Playa, Havana, Cuba
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Santiago E, Novo I, Pardiñas AF, Saura M, Wang J, Caballero A. Recent Demographic History Inferred by High-Resolution Analysis of Linkage Disequilibrium. Mol Biol Evol 2020; 37:3642-3653. [DOI: 10.1093/molbev/msaa169] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
AbstractInferring changes in effective population size (Ne) in the recent past is of special interest for conservation of endangered species and for human history research. Current methods for estimating the very recent historical Ne are unable to detect complex demographic trajectories involving multiple episodes of bottlenecks, drops, and expansions. We develop a theoretical and computational framework to infer the demographic history of a population within the past 100 generations from the observed spectrum of linkage disequilibrium (LD) of pairs of loci over a wide range of recombination rates in a sample of contemporary individuals. The cumulative contributions of all of the previous generations to the observed LD are included in our model, and a genetic algorithm is used to search for the sequence of historical Ne values that best explains the observed LD spectrum. The method can be applied from large samples to samples of fewer than ten individuals using a variety of genotyping and DNA sequencing data: haploid, diploid with phased or unphased genotypes and pseudohaploid data from low-coverage sequencing. The method was tested by computer simulation for sensitivity to genotyping errors, temporal heterogeneity of samples, population admixture, and structural division into subpopulations, showing high tolerance to deviations from the assumptions of the model. Computer simulations also show that the proposed method outperforms other leading approaches when the inference concerns recent timeframes. Analysis of data from a variety of human and animal populations gave results in agreement with previous estimations by other methods or with records of historical events.
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Affiliation(s)
- Enrique Santiago
- Departamento de Biología Funcional, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain
| | - Irene Novo
- Centro de Investigación Mariña, Departamento de Bioquímica, Genética e Inmunología, Edificio CC Experimentais, Campus de Vigo, Universidade de Vigo, Vigo, Spain
| | - Antonio F Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - María Saura
- Departamento de Mejora Genética Animal, INIA, Madrid, Spain
| | - Jinliang Wang
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - Armando Caballero
- Centro de Investigación Mariña, Departamento de Bioquímica, Genética e Inmunología, Edificio CC Experimentais, Campus de Vigo, Universidade de Vigo, Vigo, Spain
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25
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Santiago E, Caballero A. The value of targeting recombination as a strategy against coronavirus diseases. Heredity (Edinb) 2020; 125:169-172. [PMID: 32606420 PMCID: PMC7325643 DOI: 10.1038/s41437-020-0337-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 01/10/2023] Open
Affiliation(s)
- Enrique Santiago
- Departamento de Biología Funcional, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain.
| | - Armando Caballero
- Centro de Investigación Mariña, Departamento de Bioquímica, Genética e Inmunología, Edificio CC Experimentais, Campus de Vigo, As Lagoas, Universidade de Vigo, Marcosende, 36310, Vigo, Spain
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26
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Estevez R, Aguado-Deblas L, Montes V, Caballero A, Bautista F. Sulfonated carbons from olive stones as catalysts in the microwave-assisted etherification of glycerol with tert-butyl alcohol. Molecular Catalysis 2020. [DOI: 10.1016/j.mcat.2020.110921] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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27
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López‐Martín A, Platero F, Caballero A, Colón G. Thermo‐Photocatalytic Methanol Reforming for Hydrogen Production over a CuPd−TiO
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Catalyst. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- A. López‐Martín
- Instituto de Ciencia de Materiales de SevillaCentro Mixto Universidad de Sevilla-CSIC) Américo Vespucio s/n. 41092 Sevilla Spain
| | - F. Platero
- Instituto de Ciencia de Materiales de SevillaCentro Mixto Universidad de Sevilla-CSIC) Américo Vespucio s/n. 41092 Sevilla Spain
| | - A. Caballero
- Instituto de Ciencia de Materiales de SevillaCentro Mixto Universidad de Sevilla-CSIC) Américo Vespucio s/n. 41092 Sevilla Spain
| | - Gerardo Colón
- Instituto de Ciencia de Materiales de SevillaCentro Mixto Universidad de Sevilla-CSIC) Américo Vespucio s/n. 41092 Sevilla Spain
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28
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López-Martín A, Caballero A, Colón G. Structural and surface considerations on Mo/ZSM-5 systems for methane dehydroaromatization reaction. Molecular Catalysis 2020. [DOI: 10.1016/j.mcat.2020.110787] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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29
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Valdés-Bango M, Meler E, Cobo T, Hernández S, Caballero A, García F, Ribera L, Guirado L, Ferrer P, Salvia D, Figueras F, Palacio M, Goncé A, López M. [A clinical management protocol for COVID-19 infection in pregnant women]. Clin Invest Ginecol Obstet 2020; 47:118-127. [PMID: 32834309 PMCID: PMC7328537 DOI: 10.1016/j.gine.2020.06.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 06/29/2020] [Indexed: 01/08/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease (COVID-19) has caused a large global outbreak and has had a major impact on health systems and societies worldwide. The generation of knowledge about the disease has occurred almost as fast as its global expansion. Very few studies have reported on the effects of the infection on maternal health, since its onset. The mother and foetus do not seem to be at particularly high risk. Nevertheless, obstetrics and maternal-foetal medicine practice have made profound changes in order to adapt to the pandemic. In addition, there are aspects specific to COVID-19 and gestation that should be known by specialists. In this review an evidenced-based protocol is presented for the management of COVID-19 in pregnancy.
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Affiliation(s)
- M. Valdés-Bango
- Servicio de Medicina Maternofetal, Centro de Medicina Maternofetal y Neonatal de Barcelona (Hospital Clínic y Hospital Sant Joan de Déu), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Centro de Investigación Biomédica en Red Enfermedades Raras (CIBER-ER), Barcelona, España
| | - E. Meler
- Servicio de Medicina Maternofetal, Centro de Medicina Maternofetal y Neonatal de Barcelona (Hospital Clínic y Hospital Sant Joan de Déu), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Centro de Investigación Biomédica en Red Enfermedades Raras (CIBER-ER), Barcelona, España
| | - T. Cobo
- Servicio de Medicina Maternofetal, Centro de Medicina Maternofetal y Neonatal de Barcelona (Hospital Clínic y Hospital Sant Joan de Déu), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Centro de Investigación Biomédica en Red Enfermedades Raras (CIBER-ER), Barcelona, España
| | - S. Hernández
- Servicio de Medicina Maternofetal, Centro de Medicina Maternofetal y Neonatal de Barcelona (Hospital Clínic y Hospital Sant Joan de Déu), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Centro de Investigación Biomédica en Red Enfermedades Raras (CIBER-ER), Barcelona, España
| | - A. Caballero
- Servicio de Anestesiología, Hospital Clínic, Universitat de Barcelona, Barcelona, España
| | - F. García
- Servicio de Enfermedades Infecciosas, Hospital Clínic, Universitat de Barcelona, Barcelona, España
| | - L. Ribera
- Servicio de Medicina Maternofetal, Centro de Medicina Maternofetal y Neonatal de Barcelona (Hospital Clínic y Hospital Sant Joan de Déu), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Centro de Investigación Biomédica en Red Enfermedades Raras (CIBER-ER), Barcelona, España
| | - L. Guirado
- Servicio de Medicina Maternofetal, Centro de Medicina Maternofetal y Neonatal de Barcelona (Hospital Clínic y Hospital Sant Joan de Déu), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Centro de Investigación Biomédica en Red Enfermedades Raras (CIBER-ER), Barcelona, España
| | - P. Ferrer
- Servicio de Medicina Maternofetal, Centro de Medicina Maternofetal y Neonatal de Barcelona (Hospital Clínic y Hospital Sant Joan de Déu), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Centro de Investigación Biomédica en Red Enfermedades Raras (CIBER-ER), Barcelona, España
| | - D. Salvia
- Servicio de Neonatología, Hospital Clínic, Universitat de Barcelona, Barcelona, España
| | - F. Figueras
- Servicio de Medicina Maternofetal, Centro de Medicina Maternofetal y Neonatal de Barcelona (Hospital Clínic y Hospital Sant Joan de Déu), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Centro de Investigación Biomédica en Red Enfermedades Raras (CIBER-ER), Barcelona, España
| | - M. Palacio
- Servicio de Medicina Maternofetal, Centro de Medicina Maternofetal y Neonatal de Barcelona (Hospital Clínic y Hospital Sant Joan de Déu), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Centro de Investigación Biomédica en Red Enfermedades Raras (CIBER-ER), Barcelona, España
| | - A. Goncé
- Servicio de Medicina Maternofetal, Centro de Medicina Maternofetal y Neonatal de Barcelona (Hospital Clínic y Hospital Sant Joan de Déu), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Centro de Investigación Biomédica en Red Enfermedades Raras (CIBER-ER), Barcelona, España
| | - M. López
- Servicio de Medicina Maternofetal, Centro de Medicina Maternofetal y Neonatal de Barcelona (Hospital Clínic y Hospital Sant Joan de Déu), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Centro de Investigación Biomédica en Red Enfermedades Raras (CIBER-ER), Barcelona, España,Autor para correspondencia
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30
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López-Cortegano E, Pouso R, Labrador A, Pérez-Figueroa A, Fernández J, Caballero A. Optimal Management of Genetic Diversity in Subdivided Populations. Front Genet 2019; 10:843. [PMID: 31572448 PMCID: PMC6753960 DOI: 10.3389/fgene.2019.00843] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 08/13/2019] [Indexed: 11/29/2022] Open
Abstract
One of the main objectives of conservation programs is the maintenance of genetic diversity because this provides the adaptive potential of populations to face new environmental challenges. Genetic diversity is generally assessed by means of neutral molecular markers, and it is usually quantified by the expected heterozygosity under Hardy-Weinberg equilibrium and the number of alleles per locus or allelic diversity. These two measures of genetic diversity are complementary because whereas the former is directly related to genetic variance for quantitative traits and, therefore, to the short-term response to selection and adaptation, the latter is more sensitive to population bottlenecks and relates more strongly to the long-term capacity of adaptation of populations. In the context of structured populations undergoing conservation programs, it is important to decide the optimum management strategy to preserve as much genetic diversity as possible while avoiding inbreeding. Here we examine, through computer simulations, the consequences of choosing a conservation strategy based on maximizing either heterozygosity or allelic diversity of single-nucleotide polymorphism haplotypes in a subdivided population. Our results suggest that maximization of allelic diversity can be more efficient in maintaining the genetic diversity of subdivided populations than maximization of expected heterozygosity because the former maintains a larger number of alleles while making a better control of inbreeding. Thus, maximization of allelic diversity should be a recommended strategy in conservation programs for structured populations.
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Affiliation(s)
- Eugenio López-Cortegano
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| | - Ramón Pouso
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| | - Adriana Labrador
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| | - Andrés Pérez-Figueroa
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain
| | - Jesús Fernández
- Departamento de Mejora Genética, Instituto de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
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Domínguez-García S, García C, Quesada H, Caballero A. Accelerated inbreeding depression suggests synergistic epistasis for deleterious mutations in Drosophila melanogaster. Heredity (Edinb) 2019; 123:709-722. [PMID: 31477803 PMCID: PMC6834575 DOI: 10.1038/s41437-019-0263-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 08/15/2019] [Accepted: 08/18/2019] [Indexed: 01/21/2023] Open
Abstract
Epistasis may have important consequences for a number of issues in quantitative genetics and evolutionary biology. In particular, synergistic epistasis for deleterious alleles is relevant to the mutation load paradox and the evolution of sex and recombination. Some studies have shown evidence of synergistic epistasis for spontaneous or induced deleterious mutations appearing in mutation-accumulation experiments. However, many newly arising mutations may not actually be segregating in natural populations because of the erasing action of natural selection. A demonstration of synergistic epistasis for naturally segregating alleles can be achieved by means of inbreeding depression studies, as deleterious recessive allelic effects are exposed in inbred lines. Nevertheless, evidence of epistasis from these studies is scarce and controversial. In this paper, we report the results of two independent inbreeding experiments carried out with two different populations of Drosophila melanogaster. The results show a consistent accelerated inbreeding depression for fitness, suggesting synergistic epistasis among deleterious alleles. We also performed computer simulations assuming different possible models of epistasis and mutational parameters for fitness, finding some of them to be compatible with the results observed. Our results suggest that synergistic epistasis for deleterious mutations not only occurs among newly arisen spontaneous or induced mutations, but also among segregating alleles in natural populations.
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Affiliation(s)
- Sara Domínguez-García
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, 36310, Vigo, Spain
| | - Carlos García
- CIBUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain
| | - Humberto Quesada
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, 36310, Vigo, Spain
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310, Vigo, Spain. .,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, 36310, Vigo, Spain.
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Yus J, Gonzalez Z, Sanchez-Herencia A, Sangiorgi A, Sangiorgi N, Gardini D, Sanson A, Galassi C, Caballero A, Morales J, Ferrari B. Semiconductor water-based inks: Miniaturized NiO pseudocapacitor electrodes by inkjet printing. Ann Ital Chir 2019. [DOI: 10.1016/j.jeurceramsoc.2019.03.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Delgado D, Sanchís R, Cecilia J, Rodríguez-Castellón E, Caballero A, Solsona B, Nieto JL. Support effects on NiO-based catalysts for the oxidative dehydrogenation (ODH) of ethane. Catal Today 2019. [DOI: 10.1016/j.cattod.2018.07.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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López-Cortegano E, Caballero A. Inferring the Nature of Missing Heritability in Human Traits Using Data from the GWAS Catalog. Genetics 2019; 212:891-904. [PMID: 31123044 PMCID: PMC6614893 DOI: 10.1534/genetics.119.302077] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/11/2019] [Indexed: 02/07/2023] Open
Abstract
Thousands of genes responsible for many diseases and other common traits in humans have been detected by Genome Wide Association Studies (GWAS) in the last decade. However, candidate causal variants found so far usually explain only a small fraction of the heritability estimated by family data. The most common explanation for this observation is that the missing heritability corresponds to variants, either rare or common, with very small effect, which pass undetected due to a lack of statistical power. We carried out a meta-analysis using data from the NHGRI-EBI GWAS Catalog in order to explore the observed distribution of locus effects for a set of 42 complex traits and to quantify their contribution to narrow-sense heritability. With the data at hand, we were able to predict the expected distribution of locus effects for 16 traits and diseases, their expected contribution to heritability, and the missing number of loci yet to be discovered to fully explain the familial heritability estimates. Our results indicate that, for 6 out of the 16 traits, the additive contribution of a great number of loci is unable to explain the familial (broad-sense) heritability, suggesting that the gap between GWAS and familial estimates of heritability may not ever be closed for these traits. In contrast, for the other 10 traits, the additive contribution of hundreds or thousands of loci yet to be found could potentially explain the familial heritability estimates, if this were the case. Computer simulations are used to illustrate the possible contribution from nonadditive genetic effects to the gap between GWAS and familial estimates of heritability.
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Affiliation(s)
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310, Spain
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Pardiñas AF, Holmans P, Pocklington AJ, Escott-Price V, Ripke S, Carrera N, Legge SE, Bishop S, Cameron D, Hamshere ML, Han J, Hubbard L, Lynham A, Mantripragada K, Rees E, MacCabe JH, McCarroll SA, Baune BT, Breen G, Byrne EM, Dannlowski U, Eley TC, Hayward C, Martin NG, McIntosh AM, Plomin R, Porteous DJ, Wray NR, Caballero A, Geschwind DH, Huckins LM, Ruderfer DM, Santiago E, Sklar P, Stahl EA, Won H, Agerbo E, Als TD, Andreassen OA, Bækvad-Hansen M, Mortensen PB, Pedersen CB, Børglum AD, Bybjerg-Grauholm J, Djurovic S, Durmishi N, Pedersen MG, Golimbet V, Grove J, Hougaard DM, Mattheisen M, Molden E, Mors O, Nordentoft M, Pejovic-Milovancevic M, Sigurdsson E, Silagadze T, Hansen CS, Stefansson K, Stefansson H, Steinberg S, Tosato S, Werge T, Collier DA, Rujescu D, Kirov G, Owen MJ, O'Donovan MC, Walters JTR. Publisher Correction: Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection. Nat Genet 2019; 51:1193. [PMID: 31160808 DOI: 10.1038/s41588-019-0450-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Antonio F Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Andrew J Pocklington
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Valentina Escott-Price
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Stephan Ripke
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Department of Psychiatry and Psychotherapy, Charité, Campus Mitte, Berlin, Germany
| | - Noa Carrera
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Sophie E Legge
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Sophie Bishop
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Darren Cameron
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Marian L Hamshere
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Jun Han
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Leon Hubbard
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Amy Lynham
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Kiran Mantripragada
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Elliott Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - James H MacCabe
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bernhard T Baune
- Discipline of Psychiatry, University of Adelaide, Adelaide, South Australia, Australia
| | - Gerome Breen
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.,NIHR Biomedical Research Centre for Mental Health, Maudsley Hospital and Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Enda M Byrne
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia.,Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Udo Dannlowski
- Department of Psychiatry and Psychotherapy, University of Münster, Münster, Germany
| | - Thalia C Eley
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Caroline Hayward
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Nicholas G Martin
- School of Psychology, University of Queensland, Brisbane, Queensland, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK.,Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Robert Plomin
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - David J Porteous
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Naomi R Wray
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia.,Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología. Facultad de Biología, Universidad de Vigo, Vigo, Spain
| | - Daniel H Geschwind
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laura M Huckins
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Douglas M Ruderfer
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Enrique Santiago
- Departamento de Biología Funcional. Facultad de Biología, Universidad de Oviedo, Oviedo, Spain
| | - Pamela Sklar
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eli A Stahl
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hyejung Won
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Esben Agerbo
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Thomas D Als
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,Department of Biomedicine- Human Genetics, Aarhus University, Aarhus, Denmark
| | - Ole A Andreassen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Marie Bækvad-Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Preben Bo Mortensen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark.,iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Carsten Bøcker Pedersen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Anders D Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,Department of Biomedicine- Human Genetics, Aarhus University, Aarhus, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Srdjan Djurovic
- NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Naser Durmishi
- Department of Child and Adolescent Psychiatry, University Clinic of Psychiatry, Skopje, Macedonia
| | - Marianne Giørtz Pedersen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Vera Golimbet
- Department of Clinical Genetics, Mental Health Research Center, Moscow, Russia
| | - Jakob Grove
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,Department of Biomedicine- Human Genetics, Aarhus University, Aarhus, Denmark.,Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - David M Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Manuel Mattheisen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,Department of Biomedicine- Human Genetics, Aarhus University, Aarhus, Denmark
| | - Espen Molden
- Center for Psychopharmacology, Diakonhjemmet Hospital, Oslo, Norway
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Teimuraz Silagadze
- Department of Psychiatry and Drug Addiction, Tbilisi State Medical University (TSMU), Tbilisi, Georgia
| | - Christine Søholm Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | | | | | | | - Sarah Tosato
- Section of Psychiatry, Department of Public Health and Community Medicine, University of Verona, Verona, Italy
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | | | - David A Collier
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.,Discovery Neuroscience Research, Eli Lilly and Company, Lilly Research Laboratories, Windlesham, UK
| | - Dan Rujescu
- Department of Psychiatry, University of Halle, Halle, Germany.,Department of Psychiatry, University of Munich, Munich, Germany
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
| | - James T R Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
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López-Cortegano E, Pérez-Figueroa A, Caballero A. metapop2: Re-implementation of software for the analysis and management of subdivided populations using gene and allelic diversity. Mol Ecol Resour 2019; 19:1095-1100. [PMID: 30938911 DOI: 10.1111/1755-0998.13015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 03/07/2019] [Accepted: 03/19/2019] [Indexed: 01/06/2023]
Abstract
Management programmes often have to make decisions based on the analysis of the genetic properties and diversity of populations. Expected heterozygosity (or gene diversity) and population structure parameters are often used to make recommendations for conservation, such as avoidance of inbreeding or migration across subpopulations. Allelic diversity, however, can also provide complementary and useful information for conservation programmes, as it is highly sensitive to population bottlenecks, and is more related to long-term selection response than heterozygosity. Here we present a completely revised and updated re-implementation of the software metapop for the analysis of diversity in subdivided populations, as well as a tool for the management and dynamic estimation of optimal contributions in conservation programmes. This new update includes computation of allelic diversity for population analysis and management, as well as a simulation mode to forecast the consequences of taking different management strategies over time. Furthermore, the new implementation in C++ includes code optimization and improved memory usage, allowing for fast analysis of large data sets including single nucleotide polymorphism markers, as well as enhanced cross-software and cross-platform compatibility.
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Affiliation(s)
- Eugenio López-Cortegano
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| | - Andrés Pérez-Figueroa
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigaciones Biomédicas (CINBIO), Universidade de Vigo, Vigo, Spain
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
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Rivas MJ, Saura M, Pérez-Figueroa A, Panova M, Johansson T, André C, Caballero A, Rolán-Alvarez E, Johannesson K, Quesada H. Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation. Sci Rep 2018; 8:16147. [PMID: 30385764 PMCID: PMC6212547 DOI: 10.1038/s41598-018-33897-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/08/2018] [Indexed: 11/17/2022] Open
Abstract
Natural selection often produces parallel phenotypic changes in response to a similar adaptive challenge. However, the extent to which parallel gene expression differences and genomic divergence underlie parallel phenotypic traits and whether they are decoupled or not remains largely unexplored. We performed a population genomic study of parallel ecological adaptation among replicate ecotype pairs of the rough periwinkle (Littorina saxatilis) at a regional geographical scale (NW Spain). We show that genomic changes underlying parallel phenotypic divergence followed a complex pattern of both repeatable differences and of differences unique to specific ecotype pairs, in which parallel changes in expression or sequence are restricted to a limited set of genes. Yet, the majority of divergent genes were divergent either for gene expression or coding sequence, but not for both simultaneously. Overall, our findings suggest that divergent selection significantly contributed to the process of parallel molecular differentiation among ecotype pairs, and that changes in expression and gene sequence underlying phenotypic divergence could, at least to a certain extent, be considered decoupled processes.
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Affiliation(s)
- María José Rivas
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - María Saura
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Andrés Pérez-Figueroa
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Marina Panova
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Tomas Johansson
- Department of Biology, University of Lund, SE-223 62, Lund, Sweden
| | - Carl André
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Emilio Rolán-Alvarez
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Kerstin Johannesson
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Humberto Quesada
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain.
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Caballero A, Palma E, Ruiz-Esteban P, Vazquez T, Sola E, Torio A, Cabello M, Lopez V, Jironda C, Duarte A, Alonso-Titos J, Hernández D. CXCR3 + Monocytes Increase Significantly in Graft Blood Compared to Peripheral Blood in Patients With Stable Kidney Graft Function. Transplant Proc 2018; 50:555-559. [PMID: 29579851 DOI: 10.1016/j.transproceed.2017.11.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 10/20/2017] [Accepted: 11/11/2017] [Indexed: 12/29/2022]
Abstract
INTRODUCTION We have recently reported that some lymphocyte populations do not maintain the same proportion in kidney graft blood as in peripheral blood, despite a stable function of the transplanted kidney. These results suggest that a comparative study between leukocyte cells from graft blood and those obtained from peripheral blood could provide information about the inflammatory state of the transplanted organ. In this work we selected the population of CD4+ lymphocytes and monocytes expressing CXCR3 to test this hypothesis. MATERIAL AND METHODS The study was performed by flow cytometry during month 3, 6, and 12 after transplantation in 58 patients who received an isolated kidney transplant and the same immunosuppressive regimen. The peripheral blood sample was obtained by venipuncture and the graft blood by fine needle aspiration. RESULTS We found a significant percentage decrease in CXCR3+ monocytes throughout the first year of transplantation in peripheral blood (15.9 ± 20.7 vs. 12.6 ± 12.4 vs. 6.3 ± 9.0, at 3, 6, and 12 months, respectively; P = .001), whereas the percentage of CXCR3+ monocytes in graft blood did not change over this period. This situation resulted in a significant percentage difference between the CXCR3+ monocytes from the graft blood and those from the peripheral blood at the sixth (15.8 ± 8.1 vs. 12.6 ± 12.4, respectively; P = .008) and 12th months (12.9 ± 8.1 vs. 6.3 ± 9.0, respectively; P < .001). CONCLUSIONS Therefore, we can conclude that the significant percentage increase of CXCR3+ monocytes in graft blood with respect to peripheral blood suggests the presence of inflammatory activity despite renal function being stable during the second half of the first year post-transplantation.
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Affiliation(s)
- A Caballero
- Immunology Department, Regional University Hospital of Malaga and University of Malaga, IBIMA, REDINREN (RD16/0009/0006), Malaga, Spain
| | - E Palma
- Nephrology Department, Regional University Hospital of Malaga and University of Malaga, IBIMA, REDINREN (RD16/0009/0006), Malaga, Spain
| | - P Ruiz-Esteban
- Immunology Department, Complejo Hospitalario General Universitario de Albacete, Albacete, Spain
| | - T Vazquez
- Nephrology Department, Regional University Hospital of Malaga and University of Malaga, IBIMA, REDINREN (RD16/0009/0006), Malaga, Spain
| | - E Sola
- Nephrology Department, Regional University Hospital of Malaga and University of Malaga, IBIMA, REDINREN (RD16/0009/0006), Malaga, Spain
| | - A Torio
- Immunology Department, Complejo Hospitalario General Universitario de Albacete, Albacete, Spain
| | - M Cabello
- Nephrology Department, Regional University Hospital of Malaga and University of Malaga, IBIMA, REDINREN (RD16/0009/0006), Malaga, Spain
| | - V Lopez
- Nephrology Department, Regional University Hospital of Malaga and University of Malaga, IBIMA, REDINREN (RD16/0009/0006), Malaga, Spain
| | - C Jironda
- Nephrology Department, Regional University Hospital of Malaga and University of Malaga, IBIMA, REDINREN (RD16/0009/0006), Malaga, Spain
| | - A Duarte
- Nephrology Department, Regional University Hospital of Malaga and University of Malaga, IBIMA, REDINREN (RD16/0009/0006), Malaga, Spain
| | - J Alonso-Titos
- Nephrology Department, Regional University Hospital of Malaga and University of Malaga, IBIMA, REDINREN (RD16/0009/0006), Malaga, Spain
| | - D Hernández
- Nephrology Department, Regional University Hospital of Malaga and University of Malaga, IBIMA, REDINREN (RD16/0009/0006), Malaga, Spain.
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Pardiñas AF, Holmans P, Pocklington AJ, Escott-Price V, Ripke S, Carrera N, Legge SE, Bishop S, Cameron D, Hamshere ML, Han J, Hubbard L, Lynham A, Mantripragada K, Rees E, MacCabe JH, McCarroll SA, Baune BT, Breen G, Byrne EM, Dannlowski U, Eley TC, Hayward C, Martin NG, McIntosh AM, Plomin R, Porteous DJ, Wray NR, Caballero A, Geschwind DH, Huckins LM, Ruderfer DM, Santiago E, Sklar P, Stahl EA, Won H, Agerbo E, Als TD, Andreassen OA, Bækvad-Hansen M, Mortensen PB, Pedersen CB, Børglum AD, Bybjerg-Grauholm J, Djurovic S, Durmishi N, Pedersen MG, Golimbet V, Grove J, Hougaard DM, Mattheisen M, Molden E, Mors O, Nordentoft M, Pejovic-Milovancevic M, Sigurdsson E, Silagadze T, Hansen CS, Stefansson K, Stefansson H, Steinberg S, Tosato S, Werge T, Collier DA, Rujescu D, Kirov G, Owen MJ, O'Donovan MC, Walters JTR. Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection. Nat Genet 2018; 50:381-389. [PMID: 29483656 PMCID: PMC5918692 DOI: 10.1038/s41588-018-0059-2] [Citation(s) in RCA: 944] [Impact Index Per Article: 157.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/07/2018] [Indexed: 12/13/2022]
Abstract
Schizophrenia is a debilitating psychiatric condition often associated with poor quality of life and decreased life expectancy. Lack of progress in improving treatment outcomes has been attributed to limited knowledge of the underlying biology, although large-scale genomic studies have begun to provide insights. We report a new genome-wide association study of schizophrenia (11,260 cases and 24,542 controls), and through meta-analysis with existing data we identify 50 novel associated loci and 145 loci in total. Through integrating genomic fine-mapping with brain expression and chromosome conformation data, we identify candidate causal genes within 33 loci. We also show for the first time that the common variant association signal is highly enriched among genes that are under strong selective pressures. These findings provide new insights into the biology and genetic architecture of schizophrenia, highlight the importance of mutation-intolerant genes and suggest a mechanism by which common risk variants persist in the population.
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Affiliation(s)
- Antonio F Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Andrew J Pocklington
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Valentina Escott-Price
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Stephan Ripke
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry and Psychotherapy, Charité, Campus Mitte, Berlin, Germany
| | - Noa Carrera
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Sophie E Legge
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Sophie Bishop
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Darren Cameron
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Marian L Hamshere
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Jun Han
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Leon Hubbard
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Amy Lynham
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Kiran Mantripragada
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Elliott Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - James H MacCabe
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bernhard T Baune
- Discipline of Psychiatry, University of Adelaide, Adelaide, South Australia, Australia
| | - Gerome Breen
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR Biomedical Research Centre for Mental Health, Maudsley Hospital and Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Enda M Byrne
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Udo Dannlowski
- Department of Psychiatry and Psychotherapy, University of Münster, Münster, Germany
| | - Thalia C Eley
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Caroline Hayward
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Nicholas G Martin
- School of Psychology, University of Queensland, Brisbane, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Robert Plomin
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - David J Porteous
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Naomi R Wray
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología. Facultad de Biología, Universidad de Vigo, Vigo, Spain
| | - Daniel H Geschwind
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laura M Huckins
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Douglas M Ruderfer
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Enrique Santiago
- Departamento de Biología Funcional. Facultad de Biología, Universidad de Oviedo, Oviedo, Spain
| | - Pamela Sklar
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eli A Stahl
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hyejung Won
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Esben Agerbo
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Thomas D Als
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Ole A Andreassen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Marie Bækvad-Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Preben Bo Mortensen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Carsten Bøcker Pedersen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Anders D Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Srdjan Djurovic
- NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Naser Durmishi
- Department of Child and Adolescent Psychiatry, University Clinic of Psychiatry, Skopje, Macedonia
| | - Marianne Giørtz Pedersen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Vera Golimbet
- Department of Clinical Genetics, Mental Health Research Center, Moscow, Russia
| | - Jakob Grove
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - David M Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Manuel Mattheisen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Espen Molden
- Center for Psychopharmacology, Diakonhjemmet Hospital, Oslo, Norway
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Teimuraz Silagadze
- Department of Psychiatry and Drug Addiction, Tbilisi State Medical University (TSMU), Tbilisi, Georgia
| | - Christine Søholm Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | | | | | | | - Sarah Tosato
- Section of Psychiatry, Department of Public Health and Community Medicine, University of Verona, Verona, Italy
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - David A Collier
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Discovery Neuroscience Research, Eli Lilly and Company, Lilly Research Laboratories, Windlesham, UK
| | - Dan Rujescu
- Department of Psychiatry, University of Halle, Halle, Germany
- Department of Psychiatry, University of Munich, Munich, Germany
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
| | - James T R Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
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Rodríguez-Gómez A, Platero F, Caballero A, Colón G. Improving the direct synthesis of hydrogen peroxide from hydrogen and oxygen over Au-Pd/SBA-15 catalysts by selective functionalization. Molecular Catalysis 2018. [DOI: 10.1016/j.mcat.2017.10.034] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Monahan R, Caballero A, Reddy U, Stoll B, Silver B, Saade G, Dudley D. 198: Inadequate prenatal care increases the risk for stillbirth. Am J Obstet Gynecol 2018. [DOI: 10.1016/j.ajog.2017.10.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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42
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Martorell A, Caballero A, González Lama Y, Jiménez-Gallo D, Lázaro Serrano M, Miranda J, Pascual JC, Salgado-Boquete L, Marín-Jiménez I. Management of patients with hidradenitis suppurativa. Actas Dermosifiliogr 2017; 107 Suppl 2:32-42. [PMID: 28081768 DOI: 10.1016/s0001-7310(17)30007-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Hidradenitis suppurativa (HS) is a chronic inflammatory disease with a high prevalence in the population. Treatment options are both medical and surgical. Medical treatment is based on the use of antibiotics, retinoids, and anti-inflammatory drugs, in which anti-TNFα agents (infliximab y adalimumab) play a central role in the treatment of moderate-to-severe HS and enjoy the highest level of scientific support. Currently, adalimumab is the only drug approved in the summary of product characteristics for the treatment of this disease. Due to the scarcity of clinical trials in HS, there is still no therapeutic guideline backed by solid evidence and the evidence for most drugs is low. However, early treatment in patients with HS would probably reduce the complications of this disease. This review analyses the distinct treatments used in this dermatological disease and provides a therapeutic algorithm with different treatment options.
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Affiliation(s)
- A Martorell
- Servicio de Dermatología, Hospital de Manises, Valencia, España.
| | - A Caballero
- Servicio de Gastroenterología, Hospital General Universitario Gregorio Marañón, Madrid, España
| | - Y González Lama
- Unidad de Enfermedad Inflamatoria Intestinal, Servicio de Aparato Digestivo, Hospital Universitario Puerta de Hierro, Majadahonda, Madrid, España
| | - D Jiménez-Gallo
- Unidad de Gestión Clínica de Dermatología Médico-Quirúrgica y Venereología, Hospital Universitario Puerta del Mar, Servicio Andaluz de Salud, Cádiz, España
| | - M Lázaro Serrano
- Servicio de Dermatología, Hospital Universitario Basurto, Bilbao, España
| | - J Miranda
- Servicio de Gastroenterología, Hospital General Universitario Gregorio Marañón, Madrid, España
| | - J C Pascual
- Servicio de Dermatología, Hospital General de Alicante, Alicante, España
| | - L Salgado-Boquete
- Servicio de Dermatología, Complejo Hospitalario Universitario de Pontevedra, Pontevedra, España
| | - I Marín-Jiménez
- Servicio de Gastroenterología, Hospital General Universitario Gregorio Marañón, Madrid, España
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Gonzales-Gustavson E, Timoneda N, Fernandez-Cassi X, Caballero A, Abril JF, Buti M, Rodriguez-Frias F, Girones R. Identification of sapovirus GV.2, astrovirus VA3 and novel anelloviruses in serum from patients with acute hepatitis of unknown aetiology. PLoS One 2017; 12:e0185911. [PMID: 28982120 PMCID: PMC5628893 DOI: 10.1371/journal.pone.0185911] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/21/2017] [Indexed: 12/14/2022] Open
Abstract
Hepatitis is a general term meaning inflammation of the liver, which can be caused by a variety of viruses. However, a substantial number of cases remain with unknown aetiology. We analysed the serum of patients with clinical signs of hepatitis using a metagenomics approach to characterize their viral species composition. Four pools of patients with hepatitis without identified aetiological agents were evaluated. Additionally, one pool of patients with hepatitis E (HEV) and pools of healthy volunteers were included as controls. A high diversity of anelloviruses, including novel sequences, was found in pools from patients with hepatitis of unknown aetiology. Moreover, viruses recently associated with gastroenteritis as sapovirus GV.2 and astrovirus VA3 were also detected only in those pools. Besides, most of the HEV genome was recovered from the HEV pool. Finally, GB virus C and human endogenous retrovirus were found in the HEV and healthy pools. Our study provides an overview of the virome in serum from hepatitis patients suggesting a potential role of these viruses not previously described in cases of hepatitis. However, further epidemiologic studies are necessary to confirm their contribution to the development of hepatitis.
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Affiliation(s)
- Eloy Gonzales-Gustavson
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - N. Timoneda
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
- Computational Genomics Lab, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain
| | - X. Fernandez-Cassi
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - A. Caballero
- Hospital Universitari Vall d’Hebron and CIBEREHD del Instituto Carlos III, Barcelona, Catalonia, Spain
| | - J. F. Abril
- Computational Genomics Lab, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain
| | - M. Buti
- Hospital Universitari Vall d’Hebron and CIBEREHD del Instituto Carlos III, Barcelona, Catalonia, Spain
| | - F. Rodriguez-Frias
- Hospital Universitari Vall d’Hebron and CIBEREHD del Instituto Carlos III, Barcelona, Catalonia, Spain
| | - R. Girones
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
- * E-mail:
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Abid Charef S, Affoune AM, Caballero A, Cruz-Yusta M, Morales J. Simultaneous recovery of Zn and Mn from used batteries in acidic and alkaline mediums: A comparative study. Waste Manag 2017; 68:518-526. [PMID: 28669497 DOI: 10.1016/j.wasman.2017.06.048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/25/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
A parallel study of acidic and alkaline leaching for the recovery of Mn and Zn from spent alkaline batteries is outlined. Using H2SO4 as solvent and selecting appropriate conditions of temperature and concentration, all residues were dissolved except carbon. The separation and recovery of the two components were performed by electrodeposition with satisfactory results at pH values above 4 (current efficiency above 70% for Zn and Mn) but rather lower efficiencies as the pH decreased. Most of the Zn was selectively dissolved by alkaline leaching using a 6.5M NaOH solution, and its recovery was examined by means of both electrochemical and chemical processes. The expected formation of pure Zn by electrowinning failed due to the formation of ZnO, the content of which was highly dependent on the electrodeposition time. For short periods, Zn was the main component. For longer periods the electrodeposit consisted of agglomerated microparticles of ZnO with a minor fraction of Zn metal (barely 3% as measured by X-ray diffraction). A chemical reaction of the element with oxygen released at the anode surface might be responsible for its conversion to ZnO. A simple chemical route is described for the first time for the direct conversion of Zn(OH)42- solution to nanostructured ZnO by lowering the pH to values around 12 using 2M HCl solution.
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Affiliation(s)
- S Abid Charef
- Laboratoire d'Analyses Industrielles et Génie des Matériaux, Département de Génie des Procédés, Faculté des Sciences et de la Technologie, Université 8 Mai 1945 Guelma, Algeria.
| | - A M Affoune
- Laboratoire d'Analyses Industrielles et Génie des Matériaux, Département de Génie des Procédés, Faculté des Sciences et de la Technologie, Université 8 Mai 1945 Guelma, Algeria
| | - A Caballero
- Dpto. Química Inorgánica, Instituto de Química Fina y Nanoquímica, Universidad de Córdoba, 14071 Córdoba, Spain
| | - M Cruz-Yusta
- Dpto. Química Inorgánica, Instituto de Química Fina y Nanoquímica, Universidad de Córdoba, 14071 Córdoba, Spain
| | - J Morales
- Dpto. Química Inorgánica, Instituto de Química Fina y Nanoquímica, Universidad de Córdoba, 14071 Córdoba, Spain.
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Pérez-Pereira N, Quesada H, Caballero A. Can parallel ecological speciation be detected with phylogenetic analyses? Mol Phylogenet Evol 2017; 116:149-156. [PMID: 28870507 DOI: 10.1016/j.ympev.2017.08.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 07/26/2017] [Accepted: 08/31/2017] [Indexed: 11/25/2022]
Abstract
Distinguishing parallel divergence from vicariance scenarios is crucial to establish the determinism of natural selection in the formation of new species. It has been proposed that phylogenetic methods can be used to disentangle a single origin in allopatry and multiple origins in sympatry for ecological speciation. However, a key issue is to what extent introgression in a patchy environment may complicate the distinction between both origins through the analysis of variation at neutral markers. While divergence at environmentally-based selected loci retains the initial correlation with ecological variables, such association may be lost at neutral loci unlinked to any selected locus. Thus, neutral divergence might reflect in the long-term the molecular fingerprint of isolation by distance regardless of the model of speciation considered, and a question arises as to whether phylogenetic analyses of neutral markers are able or not to retrieve the signals acquired in the ancestral populations. Here, we use computer simulations to show that the detection of the original signal using a phylogenetic method strongly depends on the migration rates among populations. Recombination accelerates the loss of the initial phylogenetic signal, but this effect is rather small compared with the effect of migration, and only substantial when recombination is very large. For model species with reduced gene flow between distant populations and between populations adapted to different habitats, the phylogenetic approach is able to distinguish a single origin in allopatry from multiple origins in sympatry.
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Affiliation(s)
- Noelia Pérez-Pereira
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Pontevedra, Spain
| | - Humberto Quesada
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Pontevedra, Spain
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Pontevedra, Spain.
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Mercadal S, Vidal N, López-Parra M, Ibañez M, Caldú R, Bobillo S, Barceló I, García E, Martinez P, Cacabelos P, Dlouhy I, Sancho J, Muntañola A, Gómez L, Erro E, Gállego J, Salar A, Caballero A, Solé M, Huertas N, Estela J, Baron M, Barbero N, González-Barca E, Graus F, Velasco R. Initial management of primary central nervous system lymphoma in Spain in the last decade. The experience of the GELTAMO and Spanish neuro-oncology groups. Hematol Oncol 2017. [DOI: 10.1002/hon.2439_107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- S. Mercadal
- Hematology; Catalan Institute of Oncology. Hospital Duran i Reynals., L'Hospitalet de Llobregat; Barcelona Spain
| | - N. Vidal
- Pathology; Hospital de Bellvitge, L'Hospitalet de Llobregat; Barcelona Spain
| | - M. López-Parra
- Hematology; Hospital Universitario de Salamanca; Salamanca Spain
| | - M. Ibañez
- Neurology; Hospital Universitario i Politècnic La Fe; Valencia Spain
| | - R. Caldú
- Neurology; Hospital Universitario Miguel Servet; Zaragoza Spain
| | - S. Bobillo
- Hematology; Hospital Vall d'Hebrón; Barcelona Spain
| | - I. Barceló
- Neurology; Hospital Universitario Son Espases; Palma de Mallorca Spain
| | - E. García
- Neurology; Hospital Universitario Virgen de la Arrixaca; Murcia Spain
| | - P. Martinez
- Hematology; Hospital Universitario Doce de Octubre; Madrid Spain
| | - P. Cacabelos
- Neurology; Complejo hospitalario Santiago Compostela; Santiago Compostela Spain
| | - I. Dlouhy
- Hematology; Hospital Clínic; Barcelona Spain
| | - J. Sancho
- Hematology; ICO. Hospital Germans Trias i Pujol; Badalona Spain
| | - A. Muntañola
- Hematology; Hospital Mutua de Terrassa; Terrassa Spain
| | - L. Gómez
- Neurology; Hospital Quirón; Madrid Spain
| | - E. Erro
- Neurology; Hospital de Navarra; Pamplona Spain
| | - J. Gállego
- Neurology; Clínica Universitaria de Navarra; Pamplona Spain
| | - A. Salar
- Hematology; Hospital del Mar; Barcelona Spain
| | - A. Caballero
- Hematology; Hospital de Sant Pau; Barcelona Spain
| | - M. Solé
- Hematology; Hospital Virgen del Rocío; Sevilla Spain
| | - N. Huertas
- Neurology; Hospiatl Severo Ochoa; Leganés Spain
| | - J. Estela
- Neurology; Hospital Parc Taulí; Sabadell Spain
| | - M. Baron
- Neurology; Hospital Fundación Alcorcón; Alcorcón Spain
| | - N. Barbero
- Neurology; Hospital Rey Juan Carlos; Móstoles Spain
| | - E. González-Barca
- Hematology; Catalan Institute of Oncology. Hospital Duran i Reynals., L'Hospitalet de Llobregat; Barcelona Spain
| | - F. Graus
- Hematology; Hospital Clínic; Barcelona Spain
| | - R. Velasco
- Neurology; Hospital de Bellvitge, L'Hospitalet de Llobregat; Barcelona Spain
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Affiliation(s)
- Armando Caballero
- Institute of Cell, Animal and Population Biology; University of Edinburgh; West Mains Road Edinburgh EH9 3JT UK
| | - William G. Hill
- Institute of Cell, Animal and Population Biology; University of Edinburgh; West Mains Road Edinburgh EH9 3JT UK
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Caballero A, Bravo I, Wang J. Inbreeding load and purging: implications for the short-term survival and the conservation management of small populations. Heredity (Edinb) 2017; 118:177-185. [PMID: 27624114 PMCID: PMC5234482 DOI: 10.1038/hdy.2016.80] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 06/14/2016] [Accepted: 07/25/2016] [Indexed: 12/11/2022] Open
Abstract
Using computer simulations, we evaluate the effects of genetic purging of inbreeding load in small populations, assuming genetic models of deleterious mutations which account for the typical amount of load empirically observed. Our results show that genetic purging efficiently removes the inbreeding load of both lethal and non-lethal mutations, reducing the amount of inbreeding depression relative to that expected without selection. We find that the minimum effective population size to avoid severe inbreeding depression in the short term is of the order of Ne≈70 for a wide range of species' reproductive rates. We also carried out simulations of captive breeding populations where two contrasting management methods are performed, one avoiding inbreeding (equalisation of parental contributions (EC)) and the other forcing it (circular sib mating (CM)). We show that, for the inbreeding loads considered, CM leads to unacceptably high extinction risks and, as a result, to lower genetic diversity than EC. Thus we conclude that methods aimed at enhancing purging by intentional inbreeding should not be generally advised in captive breeding conservation programmes.
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Affiliation(s)
- A Caballero
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo (Pontevedra), Spain
| | - I Bravo
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo (Pontevedra), Spain
| | - J Wang
- Institute of Zoology, Zoological Society of London, London, UK
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Hernández-Rentero C, Vargas O, Caballero A, Morales J, Martín F. Solvothermal-induced 3D graphene networks: Role played by the structural and textural properties on lithium storage. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.11.057] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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50
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Santiago E, Caballero A. Joint Prediction of the Effective Population Size and the Rate of Fixation of Deleterious Mutations. Genetics 2016; 204:1267-1279. [PMID: 27672094 PMCID: PMC5105856 DOI: 10.1534/genetics.116.188250] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 09/20/2016] [Indexed: 11/18/2022] Open
Abstract
Mutation, genetic drift, and selection are considered the main factors shaping genetic variation in nature. There is a lack, however, of general predictions accounting for the mutual interrelation between these factors. In the context of the background selection model, we provide a set of equations for the joint prediction of the effective population size and the rate of fixation of deleterious mutations, which are applicable both to sexual and asexual species. For a population of N haploid individuals and a model of deleterious mutations with effect s appearing with rate U in a genome L Morgans long, the asymptotic effective population size (Ne) and the average number of generations (T) between consecutive fixations can be approximated by [Formula: see text] and [Formula: see text] The solution is applicable to Muller's ratchet, providing satisfactory approximations to the rate of accumulation of mutations for a wide range of parameters. We also obtain predictions of the effective size accounting for the expected nucleotide diversity. Predictions for sexual populations allow for outlining the general conditions where mutational meltdown occurs. The equations can be extended to any distribution of mutational effects and the consideration of hotspots of recombination, showing that Ne is rather insensitive and not proportional to changes in N for many combinations of parameters. This could contribute to explain the observed small differences in levels of polymorphism between species with very different census sizes.
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Affiliation(s)
- Enrique Santiago
- Departamento de Biología Funcional, Facultad de Biología, Universidad de Oviedo, 33071 Oviedo, Spain
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Spain
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