DNA damage and its association with early-life exposome: Gene-environment analysis in Colombian children under five years old.

Environmental exposures and gene-exposure interactions are the major causes of some diseases. Early-life exposome studies are needed to elucidate the role of environmental exposures and their complex interactions with biological mechanisms involved in childhood health. This study aimed to determine the contribution of early-life exposome to DNA damage and the modifying effect of genetic polymorphisms involved in air pollutants metabolism, antioxidant defense, and DNA repair. We conducted a cohort study in 416 Colombian children under five years. Blood samples at baseline were collected to measure DNA damage by the Comet assay and to determine GSTT1, GSTM1, CYP1A1, H2AX, OGG1, and SOD2 genetic polymorphisms. The exposome was estimated using geographic information systems, remote sensing, LUR models, and questionnaires. The association exposome-DNA damage was estimated using the Elastic Net linear regression with log link. Our results suggest that exposure to PM2.5 one year before the blood draw (BBD) (0.83, 95 %CI: 0.76; 0.91), soft drinks consumption (0.94, 0.89; 0.98), and GSTM1 null genotype (0.05, 0.01; 0.36) diminished the DNA damage, whereas exposure to PM2.5 one-week BBD (1.18, 1.06; 1.32), NO2 lag-5 days BBD (1.27, 1.18; 1.36), in-house cockroaches (1.10, 1.00; 1.21) at the recruitment, crowding at home (1.34, 1.08; 1.67) at the recruitment, cereal consumption (1.11, 1.04; 1.19) and H2AX (AG/GG vs. AA) (1.44, 1.11; 1.88) increased the DNA damage. The interactions between H2AX (AG/GG vs. AA) genotypes with crowding and PM2.5 one week BBD, GSTM1 (null vs. present) with humidity at the first year of life, and OGG1 (SC/CC vs. SS) with walkability at the first year of life were significant. The early-life exposome contributes to elucidating the effect of environmental exposures on DNA damage in Colombian children under five years old. The exposome-DNA damage effect appears to be modulated by genetic variants in DNA repair and antioxidant defense enzymes.

Early-life external exposome in children 2-5 years old in Colombia.

Exposome studies are advancing in high-income countries to understand how multiple environmental exposures impact health. However, there is a significant research gap in low- and middle-income and tropical countries. We aimed to describe the spatiotemporal variation of the external exposome, its correlation structure between and within exposure groups, and its dimensionality. A one-year follow-up cohort study of 506 children under 5 in two cities in Colombia was conducted to evaluate asthma, acute respiratory infections, and DNA damage. We examined 48 environmental exposures during pregnancy and 168 during childhood in eight exposure groups, including atmospheric pollutants, natural spaces, meteorology, built environment, traffic, indoor exposure, and socioeconomic capital. The exposome was estimated using geographic information systems, remote sensing, spatiotemporal modeling, and questionnaires. The median age of children at study entry was 3.7 years (interquartile range: 2.9-4.3). Air pollution and natural spaces exposure decreased from pregnancy to childhood, while socioeconomic capital increased. The highest median correlations within exposure groups were observed in meteorology (r = 0.85), traffic (r = 0.83), and atmospheric pollutants (r = 0.64). Important correlations between variables from different exposure groups were found, such as atmospheric pollutants and meteorology (r = 0.76), natural spaces (r = -0.34), and the built environment (r = 0.53). Twenty principal components explained 70%, and 57 explained 95% of the total variance in the childhood exposome. Our findings show that there is an important spatiotemporal variation in the exposome of children under 5. This is the first characterization of the external exposome in urban areas of Latin America and highlights its complexity, but also the need to better characterize and understand the exposome in order to optimize its analysis and applications in local interventions aimed at improving the health conditions and well-being of the child population and contributing to environmental health decision-making.

Characterization of the external exposome and its contribution to the clinical respiratory and early biological effects in children: The PROMESA cohort study protocol.

BACKGROUND: Air pollution contains a mixture of different pollutants from multiple sources. However, the interaction of these pollutants with other environmental exposures, as well as their harmful effects on children under five in tropical countries, is not well known. OBJECTIVE: This study aims to characterize the external exposome (ambient and indoor exposures) and its contribution to clinical respiratory and early biological effects in children. MATERIALS AND METHODS: A cohort study will be conducted on children under five (n = 500) with a one-year follow-up. Enrolled children will be followed monthly (phone call) and at months 6 and 12 (in person) post-enrolment with upper and lower Acute Respiratory Infections (ARI) examinations, asthma development, asthma control, and genotoxic damage. The asthma diagnosis will be pediatric pulmonologist-based and a standardized protocol will be used. Exposure, effect, and susceptibility biomarkers will be measured on buccal cells samples. For environmental exposures PM2.5 will be sampled, and questionnaires, geographic information, dispersion models and Land Use Regression models for PM2.5 and NO2 will be used. Different statistical methods that include Bayesian and machine learning techniques will be used for the ambient and indoor exposures-and outcomes. This study was approved by the ethics committee at Universidad Pontificia Bolivariana. EXPECTED STUDY OUTCOMES/FINDINGS: To estimate i) The toxic effect of particulate matter transcending the approach based on pollutant concentration levels; ii) The risk of developing an upper and lower ARI, based on different exposure windows; iii) A baseline of early biological damage in children under five, and describe its progression after a one-year follow-up; and iv) How physical and chemical PM2.5 characteristics influence toxicity and children's health.

[Mechanical ventilator test protocol for care of patients with COVID-19 in porcine model]. / Protocolo de prueba de ventilador mecánico para atención de pacientes con COVID-19 en modelo porcino.

As a result of the SARS-CoV-2 pandemic, health systems globally have seen a dramatic increase in the occupancy of intensive care units, with mechanical ventilators being a resource in high demand in the care of these patients. This article proposes a protocol for testing low-cost mechanical ventilators in pig models, as part of the development of locally manufactured biomedical equipment that can support the health crisis caused by the pandemic. The protocol addresses aspects that include the pre-test phase, anesthetic and airway management, laboratory monitoring, recovery and monitoring of the animal. This document presents to the academic community a validation protocol of a mechanical ventilator prototype in a pig specimen that can be a reference for its application and revalidation by other groups interested in the development of local and low-cost technologies.

A raíz de la pandemia generada por el SARS-CoV-2, los sistemas de salud de los distintos países han experimentado un dramático aumento en la ocupación de las unidades de cuidado intensivo y, por ende, una alta demanda de ventiladores mecánicos. En este artículo se propone un protocolo de pruebas de ventiladores mecánicos de bajo costo en modelos porcinos, como parte del desarrollo de equipos biomédicos que pueden apoyar la crisis sanitaria suscitada por la pandemia. El protocolo aborda aspectos que incluyen la fase previa a la prueba, el manejo anestésico, de vía aérea, seguimiento de laboratorio, recuperación y seguimiento del animal. Como resultado, se presenta a la comunidad académica un protocolo de validación de prototipo de ventilador mecánico en espécimen porcino como un referente para su aplicación y revalidación por parte de grupos interesados en el desarrollo de tecnologías locales de bajo costo.

Protocolo de prueba de ventilador mecánico para atención de pacientes con COVID-19 en modelo porcino / Mechanical ventilator test protocol for care of patients with COVID-19 in porcine model

RESUMEN A raíz de la pandemia generada por el SARS-CoV-2, los sistemas de salud de los distintos países han experimentado un dramático aumento en la ocupación de las unidades de cuidado intensivo y, por ende, una alta demanda de ventiladores mecánicos. En este artículo se propone un protocolo de pruebas de ventiladores mecánicos de bajo costo en modelos porcinos, como parte del desarrollo de equipos biomédicos que pueden apoyar la crisis sanitaria suscitada por la pandemia. El protocolo aborda aspectos que incluyen la fase previa a la prueba, el manejo anestésico, de vía aérea, seguimiento de laboratorio, recuperación y seguimiento del animal. Como resultado, se presenta a la comunidad académica un protocolo de validación de prototipo de ventilador mecánico en espécimen porcino como un referente para su aplicación y revalidación por parte de grupos interesados en el desarrollo de tecnologías locales de bajo costo.

ABSTRACT As a result of the SARS-CoV-2 pandemic, health systems globally have seen a dramatic increase in the occupancy of intensive care units, with mechanical ventilators being a resource in high demand in the care of these patients. This article proposes a protocol for testing low-cost mechanical ventilators in pig models, as part of the development of locally manufactured biomedical equipment that can support the health crisis caused by the pandemic. The protocol addresses aspects that include the pre-test phase, anesthetic and airway management, laboratory monitoring, recovery and monitoring of the animal. This document presents to the academic community a validation protocol of a mechanical ventilator prototype in a pig specimen that can be a reference for its application and revalidation by other groups interested in the development of local and low-cost technologies.

Protocolo de prueba de ventilador mecánico para atención de pacientes con COVID-19 en modelo porcino / Mechanical ventilator test protocol for care of patients with COVID-19 in porcine model

RESUMEN A raíz de la pandemia generada por el SARS-CoV-2, los sistemas de salud de los distintos países han experimentado un dramático aumento en la ocupación de las unidades de cuidado intensivo y, por ende, una alta demanda de ventiladores mecánicos. En este artículo se propone un protocolo de pruebas de ventiladores mecánicos de bajo costo en modelos porcinos, como parte del desarrollo de equipos biomédicos que pueden apoyar la crisis sanitaria suscitada por la pandemia. El protocolo aborda aspectos que incluyen la fase previa a la prueba, el manejo anestésico, de vía aérea, seguimiento de laboratorio, recuperación y seguimiento del animal. Como resultado, se presenta a la comunidad académica un protocolo de validación de prototipo de ventilador mecánico en espécimen porcino como un referente para su aplicación y revalidación por parte de grupos interesados en el desarrollo de tecnologías locales de bajo costo.

ABSTRACT As a result of the SARS-CoV-2 pandemic, health systems globally have seen a dramatic increase in the occupancy of intensive care units, with mechanical ventilators being a resource in high demand in the care of these patients. This article proposes a protocol for testing low-cost mechanical ventilators in pig models, as part of the development of locally manufactured biomedical equipment that can support the health crisis caused by the pandemic. The protocol addresses aspects that include the pre-test phase, anesthetic and airway management, laboratory monitoring, recovery and monitoring of the animal. This document presents to the academic community a validation protocol of a mechanical ventilator prototype in a pig specimen that can be a reference for its application and revalidation by other groups interested in the development of local and low-cost technologies.

Admixture and genetic diversity distribution patterns of non-recombining lineages of Native American ancestry in Colombian populations.

Genetic diversity of present American populations results from very complex demographic events involving different types and degrees of admixture. Through the analysis of lineage markers such as mtDNA and Y chromosome it is possible to recover the original Native American haplotypes, which remained identical since the admixture events due to the absence of recombination. However, the decrease in the effective population sizes and the consequent genetic drift effects suffered by these populations during the European colonization resulted in the loss or under-representation of a substantial fraction of the Native American lineages. In this study, we aim to clarify how the diversity and distribution of uniparental lineages vary with the different demographic characteristics (size, degree of isolation) and the different levels of admixture of extant Native groups in Colombia. We present new data resulting from the analyses of mtDNA whole control region, Y chromosome SNP haplogroups and STR haplotypes, and autosomal ancestry informative insertion-deletion polymorphisms in Colombian individuals from different ethnic and linguistic groups. The results demonstrate that populations presenting a high proportion of non-Native American ancestry have preserved nevertheless a substantial diversity of Native American lineages, for both mtDNA and Y chromosome. We suggest that, by maintaining the effective population sizes high, admixture allowed for a decrease in the effects of genetic drift due to Native population size reduction and thus resulting in an effective preservation of the Native American non-recombining lineages.

Continent-wide decoupling of Y-chromosomal genetic variation from language and geography in native South Americans.

Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Y-chromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans.

Genetic admixture estimates by Alu elements in Afro-Colombian and Mestizo populations from Antioquia, Colombia.

AIM: This work was intended to gain insights into the admixture processes occurring in Latin American populations by examining the genetic profiles of two ethnic groups from Antioquia (Colombia). SUBJECTS AND METHODS: To analyse the genetic variability, eight Alu insertions were typed in 64 Afro-Colombians and a reference group of 34 Hispanics (Mestizos). Admixture proportions were estimated using the Weighted Least Squares and the Gene Identity methods. The usefulness of the Alu elements as Ancestry Informative Markers (AIMs) was evaluated through differences in weighted allelic frequencies (delta values) and by hierarchical analysis of the molecular variance (AMOVA). RESULTS: The Afro-Colombian gene pool was largely determined by the African component (88.5-88.8%), but the most prominent feature was the null contribution of European genes. Mestizos were characterized by a major European component (60.0-63.8%) and a comparatively low proportion of Amerindian (19.2-20.7%) and African (17.0-19.3%) genes. Five of the Alu loci examined (ACE, APO, FXIIIB, PV92 and TPA25) showed an adequate resolving power to differentiate between continental groups, as indicated by delta values and AMOVA results. CONCLUSIONS: The peculiarity of the Afro-Colombian gene pool seems to be associated with intense genetic drift episodes that occurred in isolated communities founded by small groups of runaway slaves. ACE, APO, FXIIIB, PV92 and TPA25 could be efficiently utilized in studies dealing with demographic history and biogeographical ancestry in human populations.

A GEP-ISFG collaborative study on the optimization of an X-STR decaplex: data on 15 Iberian and Latin American populations.

In a collaborative work carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG), a polymerase chain reaction multiplex was optimized in order to type ten X-chromosome short tandem repeats (STRs) in a single reaction, including: DXS8378, DXS9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7133, GATA172D05, GATA31E08, and DXS7423. Using this X-decaplex, each 17 of the participating laboratories typed a population sample of approximately 200 unrelated individuals (100 males and 100 females). In this work, we report the allele frequencies for the ten X-STRs in 15 samples from Argentina (Buenos Aires, Córdoba, Río Negro, Entre Ríos, and Misiones), Brazil (São Paulo, Rio de Janeiro, Paraná, and Mato Grosso do Sul), Colombia (Antioquia), Costa Rica, Portugal (Northern and Central regions), and Spain (Galicia and Cantabria). Gene diversities were calculated for the ten markers in each population and all values were above 56%. The average diversity per locus varied between 66%, for DXS7133, and 82%, for DXS6809. For this set of STRs, a high discrimination power was obtained in all populations, both in males (> or =1 in 5 x 10(5)) and females (> or =1 in 3 x 10(9)), as well as high mean exclusion chance in father/daughter duos (> or =99.953%) and in father/mother/daughter trios (> or =99.999%). Genetic distance analysis showed no significant differences between northern and central Portugal or between the two Spanish samples from Galicia and Cantabria. Inside Brazil, significant differences were found between Rio de Janeiro and the other three populations, as well as between São Paulo and Paraná. For the five Argentinean samples, significant distances were only observed when comparing Misiones with Entre Ríos and with Río Negro, the only two samples that do not differ significantly from Costa Rica. Antioquia differed from all other samples, except the one from Río Negro.

Genetic data analysis of nine STRs in two Caribbean Colombian populations: César and Guajira.

POPULATION: We have analyzed the distribution of the allele frequencies and parameters of forensic interest at nine short tandem repeat (STR) loci (CSF1PO, D3S1358, D5S818, D7S820, D13S317, FGA, TH01, TPOX, and vWA) in a sample population of 165 unrelated individuals from César and Guajira, Caribbean populations of Colombia.

Y chromosome STR haplotypes in the Caribbean city of Cartagena (Colombia).

Haplotype data were obtained from a sample of 173 unrelated male individuals from Cartagena (Colombia), for 16 Y-chromosome STRs (DYS19, DYS385, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS460, DYS461, DYS635, GATA H4 and GATA A10). No shared haplotypes were observed, demonstrating the usefulness and informative power of these Y-STRs in male lineage identification in Cartagena. Genetic distances were calculated using previously published haplotype data and the lowest values were found for the comparisons with samples of Iberian origin.

Evaluación del polimorfismo por microsatélites en individuos de Piaractus brachypomus (Characidae, Serrasalminae) provenientes del río Meta, Colombia / Polymorphism evaluation by microsatellites in individuals of Piaractus brachypomus (Characidae, Serrasalminae) from Meta river, Colombia

En este estudio, cuatro microsatélites (Pme4, Pme5, Pme20, Pme21) fueron utilizados para tipificar treinta individuos de Piaractus brachypomus, provenientes del río Meta, tributario de la cuenca del río Orinoco. Los resultados mostraron un promedio de cuatro alelos por locus; se reportan seis alelos nuevos (Pme5202, Pme5204, Pme20201, Pme20211, Pme20217 y Pme21258), no descritos en la especie de referencia Piaractus mesopotamicus; el valor promedio de heterocigosidad esperado fue de 46.8 por ciento y el observado de 54.2 por ciento. El grupo de individuos no estuvo afectado por fenómenos genéticos de poblaciones como entrada o salida de individuos, mutación o selección artificial. Estos microsatélites podrían ser utilizados para el análisis genético en esta especie, dentro de los programas de conservación y selección de reproductores en zonas de cultivo.

Y-chromosome STRs in an Antioquian (Colombia) population sample.

Haplotype data were obtained from a sample of 777 unrelated male individuals from Antioquia Department (Colombia), for eight Y-chromosome STRs (DYS19, DYS385, DYS389 I, DYS389 II, DYS390, DYS391, DYS392 and DYS393). A total of 442 different haplotypes were identified of which 334 were represented only once in the database and the most frequent haplotype was found in 32 individuals. A high haplotype diversity was found (99.45%). Genetic distances were calculated using previously published haplotype data and the lowest values were found for the comparisons with samples of lberian origin.

A Peruvian population study of eight Y-chromosome STR loci.

We have analyzed the distribution of the allele frequencies and haplotypes at eight Y-chromosomal short tandem repeat (STR) loci (DYS437, DYS438, DYS439, DYS460, DYS461, GATA A10, GATA C4 and GATA H4) in a sample population of 87 unrelated individuals from Perú.