Study of the human African genome landscape through the analysis of complete genomes

Trabajo presentado en la Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2015), celebrada en Viena del 12 al 16 de julio de 2015.Understanding the genetic diversity in humans within the African continent is pivotal to have a full picture of the demographic history of the human species. Here, we study complete genome sequeces of a diverse panel of African individuals in terms of geographical location, linguistic context and lifestyle. Most African diversity studies have mainly focused on uniparental markers or selected autosomal markers, which introduce an ascertainment bias in the analysis. The analysis of complete genomes has been poorly developed in the study of African human genomics and internal population diversity. The main goals of this study are: 1. Characterisation of the internal human diversity in Africa overcoming ascertainment bias-related problems by using complete genomes. 2. Characterization of the deepest splits in the human lineage and the processes (such as migrations and admixtures) that have shaped the current genetic map.Funded by: MINECO CGL 2013-44351-P.N

Demographic inferences from a diverse panel of African human genomes

Trabajo presentado en la Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2015), celebrada en Viena del 12 al 16 de julio de 2015.Understanding genetic variation across ethnically and geographically diverse extant African populations is of great importance for reconstructing human complex demographic history. Here, we study the recent history and relationships among 15 different African populations, by analyzing the whole-genome sequence data of 21 individuals sequenced at deep coverage covering all major contine ntal linguistic groups, ecosystems and life-styles within Africa. We detected 12 million single nucleotide substitutions, providing a rich picture of the genome diversity and population history in Africa. We observe a remarkable correlation among genetic diversity and geographic origins and recent demographic history of the individuals studied. While different hunter-gatherer groups show more differentiation compared with the rest of samples, Bantu individuals are genetically more homogeneous and present evidence of admixture with neighboring hunter-gatherer groups, depending on the geographic area. Northern African individuals are closely related to non-African populations, in agreement with a recent split of both groups and continuous gene flow. To gain in sight into the deepest split of our species, we explore if recent admixture of Pygmies and Khoesan with other populations may cover up their real diversity, becoming the human most diverse groups.N

Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations

BackgroundPopulation demography and gene flow among African groups, as well as the putative archaic introgression of ancient hominins, have been poorly explored at the genome level.ResultsHere, we examine 15 African populations covering all major continental linguistic groups, ecosystems, and lifestyles within Africa through analysis of whole-genome sequence data of 21 individuals sequenced at deep coverage. We observe a remarkable correlation among genetic diversity and geographic distance, with the hunter-gatherer groups being more genetically differentiated and having larger effective population sizes throughout most modern-human history. Admixture signals are found between neighbor populations from both hunter-gatherer and agriculturalists groups, whereas North African individuals are closely related to Eurasian populations. Regarding archaic gene flow, we test six complex demographic models that consider recent admixture as well as archaic introgression. We identify the fingerprint of an archaic introgression event in the sub-Saharan populations included in the models (similar to 4.0% in Khoisan, similar to 4.3% in Mbuti Pygmies, and similar to 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage.ConclusionThe present study represents an in-depth genomic analysis of a Pan African set of individuals, which emphasizes their complex relationships and demographic history at population level.Peer reviewe

Spontaneous reperfusion enhances succinate concentration in peripheral blood from stemi patients but its levels does not correlate with myocardial infarct size or area at risk

Cardiovascular biology; Diagnostic markers; Prognostic markersBiología cardiovascular; Marcadores de diagnóstico; Marcadores pronósticosBiologia cardiovascular; Marcadors diagnòstics; Marcadors pronòsticsSuccinate is enhanced during initial reperfusion in blood from the coronary sinus in ST-segment elevation myocardial infarction (STEMI) patients and in pigs submitted to transient coronary occlusion. Succinate levels might have a prognostic value, as they may correlate with edema volume or myocardial infarct size. However, blood from the coronary sinus is not routinely obtained in the CathLab. As succinate might be also increased in peripheral blood, we aimed to investigate whether peripheral plasma concentrations of succinate and other metabolites obtained during coronary revascularization correlate with edema volume or infarct size in STEMI patients. Plasma samples were obtained from peripheral blood within the first 10 min of revascularization in 102 STEMI patients included in the COMBAT-MI trial (initial TIMI 1) and from 9 additional patients with restituted coronary blood flow (TIMI 2). Metabolite concentrations were analyzed by 1H-NMR. Succinate concentration averaged 0.069 ± 0.0073 mmol/L in patients with TIMI flow ≤ 1 and was significantly increased in those with TIMI 2 at admission (0.141 ± 0.058 mmol/L, p < 0.05). However, regression analysis did not detect any significant correlation between most metabolite concentrations and infarct size, extent of edema or other cardiac magnetic resonance (CMR) variables. In conclusion, spontaneous reperfusion in TIMI 2 patients associates with enhanced succinate levels in peripheral blood, suggesting that succinate release increases overtime following reperfusion. However, early plasma levels of succinate and other metabolites obtained from peripheral blood does not correlate with the degree of irreversible injury or area at risk in STEMI patients, and cannot be considered as predictors of CMR variables. Trial registration: Registered at www.clinicaltrials.gov (NCT02404376) on 31/03/2015. EudraCT number: 2015-001000-58.This work was supported by the Spanish Ministry of Economy and Competitiveness, Instituto de Salud Carlos III (Grants PI17/01397 and CIBERCV) and the Spanish Society of Cardiology (Proyectos de la FEC para Investigación Básica en Cardiología 2018, Sociedad Española de Cardiología), and was cofinanced by the European Regional Development Fund (ERDF-FEDER, a way to build Europe). Antonio Rodríguez-Sinovas has a consolidated Miguel Servet contract

Bacterial co-infection at hospital admission in patients with COVID-19

Objectives: We described the current incidence and risk factors of bacterial co-infection in hospitalized patients with COVID-19. Methods: Observational cohort study was performed at the Hospital Clinic of Barcelona (February 2020-February 2021). All patients with COVID-19 who were admitted for >48 hours with microbiological sample collection and procalcitonin (PCT) determination within the first 48 hours were included. Results: A total of 1125 consecutive adults met inclusion criteria. Co-infections were microbiologically documented in 102 (9.1%) patients. Most frequent microorganisms were Streptococcus pneumoniae (79%), Staphylococcus aureus (6.8%), and Haemophilus influenzae (6.8%). Test positivity was 1% (8/803) for blood cultures, 10.1% (79/780) for pneumococcal urinary antigen test, and 11.4% (15/132) for sputum culture. Patients with PCT higher than 0.2, 0.5, 1, and 2 ng/mL had significantly more co-infections than those with lower levels (p=0.017, p=0.031, p94%

Global assessment of marine plastic exposure risk for oceanic birds

Plastic pollution is distributed patchily around the world’s oceans. Likewise, marine organisms that are vulnerable to plastic ingestion or entanglement have uneven distributions. Understanding where wildlife encounters plastic is crucial for targeting research and mitigation. Oceanic seabirds, particularly petrels, frequently ingest plastic, are highly threatened, and cover vast distances during foraging and migration. However, the spatial overlap between petrels and plastics is poorly understood. Here we combine marine plastic density estimates with individual movement data for 7137 birds of 77 petrel species to estimate relative exposure risk. We identify high exposure risk areas in the Mediterranean and Black seas, and the northeast Pacific, northwest Pacific, South Atlantic and southwest Indian oceans. Plastic exposure risk varies greatly among species and populations, and between breeding and non-breeding seasons. Exposure risk is disproportionately high for Threatened species. Outside the Mediterranean and Black seas, exposure risk is highest in the high seas and Exclusive Economic Zones (EEZs) of the USA, Japan, and the UK. Birds generally had higher plastic exposure risk outside the EEZ of the country where they breed. We identify conservation and research priorities, and highlight that international collaboration is key to addressing the impacts of marine plastic on wide-ranging species

Global assessment of marine plastic exposure risk for oceanic birds

Plastic pollution is distributed patchily around the world’s oceans. Likewise, marine organisms that are vulnerable to plastic ingestion or entanglement have uneven distributions. Understanding where wildlife encounters plastic is crucial for targeting research and mitigation. Oceanic seabirds, particularly petrels, frequently ingest plastic, are highly threatened, and cover vast distances during foraging and migration. However, the spatial overlap between petrels and plastics is poorly understood. Here we combine marine plastic density estimates with individual movement data for 7137 birds of 77 petrel species to estimate relative exposure risk. We identify high exposure risk areas in the Mediterranean and Black seas, and the northeast Pacific, northwest Pacific, South Atlantic and southwest Indian oceans. Plastic exposure risk varies greatly among species and populations, and between breeding and non-breeding seasons. Exposure risk is disproportionately high for Threatened species. Outside the Mediterranean and Black seas, exposure risk is highest in the high seas and Exclusive Economic Zones (EEZs) of the USA, Japan, and the UK. Birds generally had higher plastic exposure risk outside the EEZ of the country where they breed. We identify conservation and research priorities, and highlight that international collaboration is key to addressing the impacts of marine plastic on wide-ranging species

Measurement of the B0s→μ+μ− Branching Fraction and Effective Lifetime and Search for B0→μ+μ− Decays

A search for the rare decays Bs0→μ+μ- and B0→μ+μ- is performed at the LHCb experiment using data collected in pp collisions corresponding to a total integrated luminosity of 4.4  fb-1. An excess of Bs0→μ+μ- decays is observed with a significance of 7.8 standard deviations, representing the first observation of this decay in a single experiment. The branching fraction is measured to be B(Bs0→μ+μ-)=(3.0±0.6-0.2+0.3)×10-9, where the first uncertainty is statistical and the second systematic. The first measurement of the Bs0→μ+μ- effective lifetime, τ(Bs0→μ+μ-)=2.04±0.44±0.05  ps, is reported. No significant excess of B0→μ+μ- decays is found, and a 95% confidence level upper limit, B(B0→μ+μ-)<3.4×10-10, is determined. All results are in agreement with the standard model expectations.A search for the rare decays $B^0_s\to\mu^+\mu^-$ and $B^0\to\mu^+\mu^-$ is performed at the LHCb experiment using data collected in $pp$ collisions corresponding to a total integrated luminosity of 4.4 fb$^{-1}$. An excess of $B^0_s\to\mu^+\mu^-$ decays is observed with a significance of 7.8 standard deviations, representing the first observation of this decay in a single experiment. The branching fraction is measured to be ${\cal B}(B^0_s\to\mu^+\mu^-)=\left(3.0\pm 0.6^{+0.3}_{-0.2}\right)\times 10^{-9}$, where the first uncertainty is statistical and the second systematic. The first measurement of the $B^0_s\to\mu^+\mu^-$ effective lifetime, $\tau(B^0_s\to\mu^+\mu^-)=2.04\pm 0.44\pm 0.05$ ps, is reported. No significant excess of $B^0\to\mu^+\mu^-$ decays is found and a 95 % confidence level upper limit, ${\cal B}(B^0\to\mu^+\mu^-)<3.4\times 10^{-10}$, is determined. All results are in agreement with the Standard Model expectations

Insights into the human demographic history of Africa through whole-genome sequence analysis

Àfrica és l'origen de totes les poblacions humanes actuals, i malgrat contenir els nivells més elevats de diversitat genètica, la seva història demogràfica ha estat relativament poc estudiada, amb moltes preguntes rellevants encara obertes, com ara els escenaris d'introgressió arcaica en poblacions modernes o el debat entre continuitat o reemplaçament en les poblacions del Nord d'Àfrica. Per tal de respondre aquestes qüestions, hem analitzat genomes complets d'un panell d'individus africans divers a nivell geogràfic, ligüístic i cultural. Hem caracteritzat els llinatges humans més divergents, corresponents a grups de caçadors-recol·lectors, així com els processos demogràfics que han donat forma al mapa genètic actual, incloent-hi flux gènic intracontinental i d'Euràsia cap al nord i est d'Àfrica, i introgressió arcaica en poblacions sub-saharianes de l'oest, centre i sud del continent. El Nord d'Àfrica té una història genètica independent de la de la resta del continent, i s'hi han identificat cinc components ancestrals: subsaharià, europeu, de l'Orient Mitjà, caucasià i un component heterogeni autòcton nordafricà persistent des de l'epipaleolític.Africa is the source of worldwide human populations, and despite harboring the highest levels of genetic diversity, its complex demographic history has remained understudied for a long time, with several relevant questions remaining open, like the archaic introgression scenario or the continuity vs replacement debate in North Africa. To address these questions, we analyzed complete genome sequences from a geographically, linguistically, and culturally diverse panel of African individuals. We characterized the deepest human lineages, corresponding to hunter-gatherer groups, and the demographic processes that have shaped the current genetic map, including intra-continental admixture and backflow from Eurasia to northern and eastern Africa and archaic introgression in western, central and southern sub-Saharan populations. North Africa shows as an independent genetic history from the rest of the continent, with five different ancestries, including sub-Saharan, European, Middle Eastern, Caucasian and a heterogeneously persistent North African Epipalaeolithic component

Insights into the human demographic history of Africa through whole-genome sequence analysis

Àfrica és l'origen de totes les poblacions humanes actuals, i malgrat contenir els nivells més elevats de diversitat genètica, la seva història demogràfica ha estat relativament poc estudiada, amb moltes preguntes rellevants encara obertes, com ara els escenaris d'introgressió arcaica en poblacions modernes o el debat entre continuitat o reemplaçament en les poblacions del Nord d'Àfrica. Per tal de respondre aquestes qüestions, hem analitzat genomes complets d'un panell d'individus africans divers a nivell geogràfic, ligüístic i cultural. Hem caracteritzat els llinatges humans més divergents, corresponents a grups de caçadors-recol·lectors, així com els processos demogràfics que han donat forma al mapa genètic actual, incloent-hi flux gènic intracontinental i d'Euràsia cap al nord i est d'Àfrica, i introgressió arcaica en poblacions sub-saharianes de l'oest, centre i sud del continent. El Nord d'Àfrica té una història genètica independent de la de la resta del continent, i s'hi han identificat cinc components ancestrals: subsaharià, europeu, de l'Orient Mitjà, caucasià i un component heterogeni autòcton nordafricà persistent des de l'epipaleolític.Africa is the source of worldwide human populations, and despite harboring the highest levels of genetic diversity, its complex demographic history has remained understudied for a long time, with several relevant questions remaining open, like the archaic introgression scenario or the continuity vs replacement debate in North Africa. To address these questions, we analyzed complete genome sequences from a geographically, linguistically, and culturally diverse panel of African individuals. We characterized the deepest human lineages, corresponding to hunter-gatherer groups, and the demographic processes that have shaped the current genetic map, including intra-continental admixture and backflow from Eurasia to northern and eastern Africa and archaic introgression in western, central and southern sub-Saharan populations. North Africa shows as an independent genetic history from the rest of the continent, with five different ancestries, including sub-Saharan, European, Middle Eastern, Caucasian and a heterogeneously persistent North African Epipalaeolithic component