Genetic Ancestry Inference for Pharmacogenomics.

Genetic ancestry inference can be used to stratify patient cohorts and to model pharmacogenomic variation within and between populations. We provide a detailed guide to genetic ancestry inference using genome-wide genetic variant datasets, with an emphasis on two widely used techniques: principal components analysis (PCA) and ADMIXTURE analysis. PCA can be used for patient stratification and categorical ancestry inference, whereas ADMIXTURE is used to characterize genetic ancestry as a continuous variable. Visualization methods are critical for the interpretation of genetic ancestry inference methods, and we provide instructions for how the results of PCA and ADMIXTURE can be effectively visualized.

The Impact of Ethnicity and Genetic Ancestry on Disease Prevalence and Risk in Colombia.

Currently, the vast majority of genomic research cohorts are made up of participants with European ancestry. Genomic medicine will only reach its full potential when genomic studies become more broadly representative of global populations. We are working to support the establishment of genomic medicine in developing countries in Latin America via studies of ethnically and ancestrally diverse Colombian populations. The goal of this study was to analyze the effect of ethnicity and genetic ancestry on observed disease prevalence and predicted disease risk in Colombia. Population distributions of Colombia's three major ethnic groups - Mestizo, Afro-Colombian, and Indigenous - were compared to disease prevalence and socioeconomic indicators. Indigenous and Mestizo ethnicity show the highest correlations with disease prevalence, whereas the effect of Afro-Colombian ethnicity is substantially lower. Mestizo ethnicity is mostly negatively correlated with six high-impact health conditions and positively correlated with seven of eight common cancers; Indigenous ethnicity shows the opposite effect. Malaria prevalence in particular is strongly correlated with ethnicity. Disease prevalence co-varies across geographic regions, consistent with the regional distribution of ethnic groups. Ethnicity is also correlated with regional variation in human development, partially explaining the observed differences in disease prevalence. Patterns of genetic ancestry and admixture for a cohort of 624 individuals from Medellín were compared to disease risk inferred via polygenic risk scores (PRS). African genetic ancestry is most strongly correlated with predicted disease risk, whereas European and Native American ancestry show weaker effects. African ancestry is mostly positively correlated with disease risk, and European ancestry is mostly negatively correlated. The relationships between ethnicity and disease prevalence do not show an overall correspondence with the relationships between ancestry and disease risk. We discuss possible reasons for the divergent health effects of ethnicity and ancestry as well as the implication of our results for the development of precision medicine in Colombia.

Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields.

Previous studies have shown the sugarcane microbiome harbors diverse plant growth promoting microorganisms, including nitrogen-fixing bacteria (diazotrophs), which can serve as biofertilizers. The genomes of 22 diazotrophs from Colombian sugarcane fields were sequenced to investigate potential biofertilizers. A genome-enabled computational phenotyping approach was developed to prioritize sugarcane associated diazotrophs according to their potential as biofertilizers. This method selects isolates that have potential for nitrogen fixation and other plant growth promoting (PGP) phenotypes while showing low risk for virulence and antibiotic resistance. Intact nitrogenase (nif) genes and operons were found in 18 of the isolates. Isolates also encode phosphate solubilization and siderophore production operons, and other PGP genes. The majority of sugarcane isolates showed uniformly low predicted virulence and antibiotic resistance compared to clinical isolates. Six strains with the highest overall genotype scores were experimentally evaluated for nitrogen fixation, phosphate solubilization, and the production of siderophores, gibberellic acid, and indole acetic acid. Results from the biochemical assays were consistent and validated computational phenotype predictions. A genotypic and phenotypic threshold was observed that separated strains by their potential for PGP versus predicted pathogenicity. Our results indicate that computational phenotyping is a promising tool for the assessment of bacteria detected in agricultural ecosystems.

Plasma interleukin-6 levels correlate with survival in patients with bacterial sepsis and septic shock.

In this study, IL-6 levels were assessed as inflammatory biomarker of bacterial sepsis in patients hospitalized at the ICU of the hospital of Colombia. Materials and methods: Prospective study on 62 patients diagnosed with sepsis and septic shock. An ELISA assay was used to test serum levels of IL-6 at admission and 48 h after admission. Variables were analyzed by χ2 test (alfa <0.05). Multivariable Cox regression was used to determine the survival with the statistical program SPSS v23.00. Results: Patient's median age was 53 years old and 59.7% were male. Lung was the most common primary site of infection (43.5%), and hypertension comorbidity with higher prevalence (40%). Infection by Gram negative bacteria were significantly more frequent among patients than Gram positive (P = 0.037). Overall, survival analysis showed that 10 (16.1%) patients died with a survival median of 7.00 +4.874 (2-3) days. In patients with sepsis we detected a significant decline in the average of IL-6 serum levels after 48 h of admission [7.50 (SD: 7.00-68.00) pg/mL vs. 68.00 [SD: 7.00-300.00] pg/mL (P = 0.000). Only 25% of patients with septic shock who presented high levels of IL-6 at the time of admission and at 48 h had a survival up to 15 days (P = 0.005). Conclusion: We found significant differences between the plasma levels of IL-6 during the first 48 h after admission to the ICU among patients with sepsis and septic shock. Patients with sepsis had a significant decline in IL-6 levels, whereas in patients who developed septic shock, levels of this cytokine remained high and have a lower survival compared to those who maintained low levels of IL-6.

The Phenotypic Consequences of Genetic Divergence between Admixed Latin American Populations: Antioquia and Chocó, Colombia.

Genome-wide association studies have uncovered thousands of genetic variants that are associated with a wide variety of human traits. Knowledge of how trait-associated variants are distributed within and between populations can provide insight into the genetic basis of group-specific phenotypic differences, particularly for health-related traits. We analyzed the genetic divergence levels for 1) individual trait-associated variants and 2) collections of variants that function together to encode polygenic traits, between two neighboring populations in Colombia that have distinct demographic profiles: Antioquia (Mestizo) and Chocó (Afro-Colombian). Genetic ancestry analysis showed 62% European, 32% Native American, and 6% African ancestry for Antioquia compared with 76% African, 10% European, and 14% Native American ancestry for Chocó, consistent with demography and previous results. Ancestry differences can confound cross-population comparison of polygenic risk scores (PRS); however, we did not find any systematic bias in PRS distributions for the two populations studied here, and population-specific differences in PRS were, for the most part, small and symmetrically distributed around zero. Both genetic differentiation at individual trait-associated single nucleotide polymorphisms and population-specific PRS differences between Antioquia and Chocó largely reflected anthropometric phenotypic differences that can be readily observed between the populations along with reported disease prevalence differences. Cases where population-specific differences in genetic risk did not align with observed trait (disease) prevalence point to the importance of environmental contributions to phenotypic variance, for both infectious and complex, common disease. The results reported here are distributed via a web-based platform for searching trait-associated variants and PRS divergence levels at http://map.chocogen.com (last accessed August 12, 2020).

Ancestry effects on type 2 diabetes genetic risk inference in Hispanic/Latino populations.

BACKGROUND: Hispanic/Latino (HL) populations bear a disproportionately high burden of type 2 diabetes (T2D). The ability to predict T2D genetic risk using polygenic risk scores (PRS) offers great promise for improved screening and prevention. However, there are a number of complications related to the accurate inference of genetic risk across HL populations with distinct ancestry profiles. We investigated how ancestry affects the inference of T2D genetic risk using PRS in diverse HL populations from Colombia and the United States (US). In Colombia, we compared T2D genetic risk for the Mestizo population of Antioquia to the Afro-Colombian population of Chocó, and in the US, we compared European-American versus Mexican-American populations. METHODS: Whole genome sequences and genotypes from the 1000 Genomes Project and the ChocoGen Research Project were used for genetic ancestry inference and for T2D polygenic risk score (PRS) calculation. Continental ancestry fractions for HL genomes were inferred via comparison with African, European, and Native American reference genomes, and PRS were calculated using T2D risk variants taken from multiple genome-wide association studies (GWAS) conducted on cohorts with diverse ancestries. A correction for ancestry bias in T2D risk inference based on the frequencies of ancestral versus derived alleles was developed and applied to PRS calculations in the HL populations studied here. RESULTS: T2D genetic risk in Colombian and US HL populations is positively correlated with African and Native American ancestry and negatively correlated with European ancestry. The Afro-Colombian population of Chocó has higher predicted T2D risk than Antioquia, and the Mexican-American population has higher predicted risk than the European-American population. The inferred relative risk of T2D is robust to differences in the ancestry of the GWAS cohorts used for variant discovery. For trans-ethnic GWAS, population-specific variants and variants with same direction effects across populations yield consistent results. Nevertheless, the control for bias in T2D risk prediction confirms that explicit consideration of genetic ancestry can yield more reliable cross-population genetic risk inferences. CONCLUSIONS: T2D associations that replicate across populations provide for more reliable risk inference, and modeling population-specific frequencies of ancestral and derived risk alleles can help control for biases in PRS estimation.

Risk factors associated with pulmonary tuberculosis relapses in Cali, Colombia. / Factores de riesgo asociados con recaídas de tuberculosis pulmonar en Cali, Colombia

INTRODUCTION: Relapses in tuberculosis occur due to endogenous reactivations or exogenous reinfections and represent up to 27% of tuberculosis cases. Its importance lies in the risk of the appearance of multidrug-resistant Mycobacterium tuberculosis strains. According to the reports published in 2011 by the Colombian Instituto Nacional de Salud, there were 572 relapse cases reported in the country, i.e., a rate of 4.9%. Data of the tuberculosis control program from the Secretaría de Salud Municipal in Cali reported a relapse rate of 6%, higher than the national one, during 2013 and 2014. OBJECTIVE: To determine the risk factors associated with relapse in patients with pulmonary tuberculosis in Cali. MATERIALS AND METHODS: We conducted an observational, analytical, and case-control study (1:1), which comprised 81 cases of pulmonary tuberculosis relapses detected in 2013 and 2014. Additionally, we collected data on socio-demographic and clinical variables, as well as lifestyle and health services, to identify the potential risk factors associated with tuberculosis relapses. We used logistic regression to identify the risk factors. RESULTS: After adjustments for some variables, our multivariate logistic regression analysis showed that the body mass index (BMI) (OR=0.90, 95%CI: 0.81-0.99) and population density (OR=0.99, 95%CI: 0.98-1.00) were inversely associated with tuberculosis relapses. Alcohol consumption increased the likelihood of tuberculosis relapse (OR=5.56, 95%CI: 1.18-26.26). CONCLUSIONS: Body mass index and population density were inversely associated with pulmonary tuberculosis relapses in Cali. On the contrary, alcohol consumption increased the likelihood of tuberculosis relapses.

Introducción. Las recaídas en la tuberculosis se deben a reactivaciones endógenas o reinfecciones exógenas y alcanzan hasta el 27 % de los casos. Su importancia radica en el riesgo de aparición de cepas de Mycobacterium tuberculosis resistentes a múltiples fármacos. Según informes del Instituto Nacional de Salud de Colombia, en el 2011 se reportaron 572 recaídas, lo que representa un porcentaje del 4,9 %. Datos del programa de tuberculosis de la Secretaría de Salud Municipal de Cali registraron una tasa de recaídas del 6 % durante el 2013 y el 2014, lo que supera la tasa nacional. Objetivo. Determinar los factores asociados con la recaída en pacientes con tuberculosis pulmonar. Materiales y métodos. Se hizo un estudio observacional, analítico y de casos y controles en pacientes diagnosticados con tuberculosis pulmonar detectados entre el 2013 y el 2014. Se estudiaron las variables sociodemográficas, clínicas, de estilo de vida y las relacionadas con el programa y los factores de riesgo; se determinaron utilizando regresión logística. Resultados. Después de ajustar por otras variables, la regresión logística evidenció dos factores inversamente asociados con las recaídas: el índice de masa corporal (OR=0,90; IC95%: 0,81­0,99) y la densidad poblacional en las comunas (OR=0,99; IC95%:0,99­1,00. El consumo de alcohol aumentó la probabilidad de recaída (OR=5,56; IC95%: 1,18 ­ 26,26). Conclusiones. El índice de masa corporal y la densidad poblacional se asociaron inversamente con las recaídas por tuberculosis pulmonar en Cali. El consumo de alcohol estuvo directamente relacionado.

Risk factors associated with pulmonary tuberculosis relapses in Cali, Colombia / Factores de riesgo asociados con recaídas de tuberculosis pulmonar en Cali, Colombia

Introduction: Relapses in tuberculosis occur due to endogenous reactivations or exogenous reinfections and represent up to 27% of tuberculosis cases. Its importance lies in the risk of the appearance of multidrug-resistant Mycobacterium tuberculosis strains. According to the reports published in 2011 by the Colombian Instituto Nacional de Salud, there were 572 relapse cases reported in the country, i.e., a rate of 4.9%. Data of the tuberculosis control program from the Secretaría de Salud Municipal in Cali reported a relapse rate of 6%, higher than the national one, during 2013 and 2014. Objective: To determine the risk factors associated with relapse in patients with pulmonary tuberculosis in Cali. Materials and methods: We conducted an observational, analytical, and case-control study (1:1), which comprised 81 cases of pulmonary tuberculosis relapses detected in 2013 and 2014. Additionally, we collected data on socio-demographic and clinical variables, as well as lifestyle and health services, to identify the potential risk factors associated with tuberculosis relapses. We used logistic regression to identify the risk factors. Results: After adjustments for some variables, our multivariate logistic regression analysis showed that the body mass index (BMI) (OR=0.90, 95%CI: 0.81-0.99) and population density (OR=0.99, 95%CI: 0.98-1.00) were inversely associated with tuberculosis relapses. Alcohol consumption increased the likelihood of tuberculosis relapse (OR=5.56, 95%CI: 1.18-26.26). Conclusions: Body mass index and population density were inversely associated with pulmonary tuberculosis relapses in Cali. On the contrary, alcohol consumption increased the likelihood of tuberculosis relapses.

Introducción. Las recaídas en la tuberculosis se deben a reactivaciones endógenas o reinfecciones exógenas y alcanzan hasta el 27 % de los casos. Su importancia radica en el riesgo de aparición de cepas de Mycobacterium tuberculosis resistentes a múltiples fármacos. Según informes del Instituto Nacional de Salud de Colombia, en el 2011 se reportaron 572 recaídas, lo que representa un porcentaje del 4,9 %. Datos del programa de tuberculosis de la Secretaría de Salud Municipal de Cali registraron una tasa de recaídas del 6 % durante el 2013 y el 2014, lo que supera la tasa nacional. Objetivo. Determinar los factores asociados con la recaída en pacientes con tuberculosis pulmonar. Materiales y métodos. Se hizo un estudio observacional, analítico y de casos y controles en pacientes diagnosticados con tuberculosis pulmonar detectados entre el 2013 y el 2014. Se estudiaron las variables sociodemográficas, clínicas, de estilo de vida y las relacionadas con el programa y los factores de riesgo; se determinaron utilizando regresión logística. Resultados. Después de ajustar por otras variables, la regresión logística evidenció dos factores inversamente asociados con las recaídas: el índice de masa corporal (OR=0,90; IC95%: 0,81-0,99) y la densidad poblacional en las comunas (OR=0,99; IC95%:0,99-1,00. El consumo de alcohol aumentó la probabilidad de recaída (OR=5,56; IC95%: 1,18 - 26,26). Conclusiones. El índice de masa corporal y la densidad poblacional se asociaron inversamente con las recaídas por tuberculosis pulmonar en Cali. El consumo de alcohol estuvo directamente relacionado.

Admixture-enabled selection for rapid adaptive evolution in the Americas.

BACKGROUND: Admixture occurs when previously isolated populations come together and exchange genetic material. We hypothesize that admixture can enable rapid adaptive evolution in human populations by introducing novel genetic variants (haplotypes) at intermediate frequencies, and we test this hypothesis through the analysis of whole genome sequences sampled from admixed Latin American populations in Colombia, Mexico, Peru, and Puerto Rico. RESULTS: Our screen for admixture-enabled selection relies on the identification of loci that contain more or less ancestry from a given source population than would be expected given the genome-wide ancestry frequencies. We employ a combined evidence approach to evaluate levels of ancestry enrichment at single loci across multiple populations and multiple loci that function together to encode polygenic traits. We find cross-population signals of African ancestry enrichment at the major histocompatibility locus on chromosome 6, consistent with admixture-enabled selection for enhanced adaptive immune response. Several of the human leukocyte antigen genes at this locus, such as HLA-A, HLA-DRB51, and HLA-DRB5, show independent evidence of positive selection prior to admixture, based on extended haplotype homozygosity in African populations. A number of traits related to inflammation, blood metabolites, and both the innate and adaptive immune system show evidence of admixture-enabled polygenic selection in Latin American populations. CONCLUSIONS: The results reported here, considered together with the ubiquity of admixture in human evolution, suggest that admixture serves as a fundamental mechanism that drives rapid adaptive evolution in human populations.

Assortative Mating on Ancestry-Variant Traits in Admixed Latin American Populations.

Assortative mating is a universal feature of human societies, and individuals from ethnically diverse populations are known to mate assortatively based on similarities in genetic ancestry. However, little is currently known regarding the exact phenotypic cues, or their underlying genetic architecture, which inform ancestry-based assortative mating. We developed a novel approach, using genome-wide analysis of ancestry-specific haplotypes, to evaluate ancestry-based assortative mating on traits whose expression varies among the three continental population groups - African, European, and Native American - that admixed to form modern Latin American populations. Application of this method to genome sequences sampled from Colombia, Mexico, Peru, and Puerto Rico revealed widespread ancestry-based assortative mating. We discovered a number of anthropometric traits (body mass, height, and facial development) and neurological attributes (educational attainment and schizophrenia) that serve as phenotypic cues for ancestry-based assortative mating. Major histocompatibility complex (MHC) loci show population-specific patterns of both assortative and disassortative mating in Latin America. Ancestry-based assortative mating in the populations analyzed here appears to be driven primarily by African ancestry. This study serves as an example of how population genomic analyses can yield novel insights into human behavior.

Population Pharmacogenomics for Precision Public Health in Colombia.

While genomic approaches to precision medicine hold great promise, they remain prohibitively expensive for developing countries. The precision public health paradigm, whereby healthcare decisions are made at the level of populations as opposed to individuals, provides one way for the genomics revolution to directly impact health outcomes in the developing world. Genomic approaches to precision public health require a deep understanding of local population genomics, which is still missing for many developing countries. We are investigating the population genomics of genetic variants that mediate drug response in an effort to inform healthcare decisions in Colombia. Our work focuses on two neighboring populations with distinct ancestry profiles: Antioquia and Chocó. Antioquia has primarily European genetic ancestry followed by Native American and African components, whereas Chocó shows mainly African ancestry with lower levels of Native American and European admixture. We performed a survey of the global distribution of pharmacogenomic variants followed by a more focused study of pharmacogenomic allele frequency differences between the two Colombian populations. Worldwide, we found pharmacogenomic variants to have both unusually high minor allele frequencies and high levels of population differentiation. A number of these pharmacogenomic variants also show anomalous effect allele frequencies within and between the two Colombian populations, and these differences were found to be associated with their distinct genetic ancestry profiles. For example, the C allele of the single nucleotide polymorphism (SNP) rs4149056 [Solute Carrier Organic Anion Transporter Family Member 1B1 (SLCO1B1)∗5], which is associated with an increased risk of toxicity to a commonly prescribed statin, is found at relatively high frequency in Antioquia and is associated with European ancestry. In addition to pharmacogenomic alleles related to increased toxicity risk, we also have evidence that alleles related to dosage and metabolism have large frequency differences between the two populations, which are associated with their specific ancestries. Using these findings, we have developed and validated an inexpensive allele-specific PCR assay to test for the presence of such population-enriched pharmacogenomic SNPs in Colombia. These results serve as an example of how population-centered approaches to pharmacogenomics can help to realize the promise of precision medicine in resource-limited settings.

Genetic ancestry, admixture and health determinants in Latin America.

BACKGROUND: Modern Latin American populations were formed via genetic admixture among ancestral source populations from Africa, the Americas and Europe. We are interested in studying how combinations of genetic ancestry in admixed Latin American populations may impact genomic determinants of health and disease. For this study, we characterized the impact of ancestry and admixture on genetic variants that underlie health- and disease-related phenotypes in population genomic samples from Colombia, Mexico, Peru, and Puerto Rico. RESULTS: We analyzed a total of 347 admixed Latin American genomes along with 1102 putative ancestral source genomes from Africans, Europeans, and Native Americans. We characterized the genetic ancestry, relatedness, and admixture patterns for each of the admixed Latin American genomes, finding a spectrum of ancestry proportions within and between populations. We then identified single nucleotide polymorphisms (SNPs) with anomalous ancestry-enrichment patterns, i.e. SNPs that exist in any given Latin American population at a higher frequency than expected based on the population's genetic ancestry profile. For this set of ancestry-enriched SNPs, we inspected their phenotypic impact on disease, metabolism, and the immune system. All four of the Latin American populations show ancestry-enrichment for a number of shared pathways, yielding evidence of similar selection pressures on these populations during their evolution. For example, all four populations show ancestry-enriched SNPs in multiple genes from immune system pathways, such as the cytokine receptor interaction, T cell receptor signaling, and antigen presentation pathways. We also found SNPs with excess African or European ancestry that are associated with ancestry-specific gene expression patterns and play crucial roles in the immune system and infectious disease responses. Genes from both the innate and adaptive immune system were found to be regulated by ancestry-enriched SNPs with population-specific regulatory effects. CONCLUSIONS: Ancestry-enriched SNPs in Latin American populations have a substantial effect on health- and disease-related phenotypes. The concordant impact observed for same phenotypes across populations points to a process of adaptive introgression, whereby ancestry-enriched SNPs with specific functional utility appear to have been retained in modern populations by virtue of their effects on health and fitness.

GlobAl Distribution of GEnetic Traits (GADGET) web server: polygenic trait scores worldwide.

Human populations from around the world show striking phenotypic variation across a wide variety of traits. Genome-wide association studies (GWAS) are used to uncover genetic variants that influence the expression of heritable human traits; accordingly, population-specific distributions of GWAS-implicated variants may shed light on the genetic basis of human phenotypic diversity. With this in mind, we developed the GlobAl Distribution of GEnetic Traits web server (GADGET http://gadget.biosci.gatech.edu). The GADGET web server provides users with a dynamic visual platform for exploring the relationship between worldwide genetic diversity and the genetic architecture underlying numerous human phenotypes. GADGET integrates trait-implicated single nucleotide polymorphisms (SNPs) from GWAS, with population genetic data from the 1000 Genomes Project, to calculate genome-wide polygenic trait scores (PTS) for 818 phenotypes in 2504 individual genomes. Population-specific distributions of PTS are shown for 26 human populations across 5 continental population groups, with traits ordered based on the extent of variation observed among populations. Users of GADGET can also upload custom trait SNP sets to visualize global PTS distributions for their own traits of interest.

Genome Sequences of 15 Klebsiella sp. Isolates from Sugarcane Fields in Colombia's Cauca Valley.

Members of the Klebsiella genus promote plant growth. We report here draft whole-genome sequences for 15 Klebsiella sp. isolates from sugarcane fields in the Cauca Valley of Colombia. The genomes of these isolates were characterized as part of a broader effort to evaluate their utility as endemic plant growth-promoting biofertilizers.

Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline.

The dinitrogenase reductase gene (nifH) is the most widely established molecular marker for the study of nitrogen-fixing prokaryotes in nature. A large number of PCR primer sets have been developed for nifH amplification, and the effective deployment of these approaches should be guided by a rapid, easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this study, we advance the state of the art for nifH analysis by evaluating nifH primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline. The developed amplicon sequencing workflow is a three-stage PCR-based approach that uses established technologies for incorporating sample-specific barcode sequences and sequencing adapters. Based on our primer evaluation, we recommend the Ando primer set be used with a modified annealing temperature of 58°C, as this approach captured the largest diversity of nifH templates, including paralog cluster IV/V sequences. To improve nifH sequence analysis, we developed a computational pipeline which infers taxonomy and optionally filters out paralog sequences. In addition, we employed an empirical model to derive optimal operational taxonomic unit (OTU) cutoffs for the nifH gene at the species, genus, and family levels. A comprehensive workflow script named TaxADivA (TAXonomy Assignment and DIVersity Assessment) is provided to ease processing and analysis of nifH amplicons. Our approach is then validated through characterization of diazotroph communities across environmental gradients in beach sands impacted by the Deepwater Horizon oil spill in the Gulf of Mexico, in a peat moss-dominated wetland, and in various plant compartments of a sugarcane field.IMPORTANCE Nitrogen availability often limits ecosystem productivity, and nitrogen fixation, exclusive to prokaryotes, comprises a major source of nitrogen input that sustains food webs. The nifH gene, which codes for the iron protein of the nitrogenase enzyme, is the most widely established molecular marker for the study of nitrogen-fixing microorganisms (diazotrophs) in nature. In this study, a flexible sequencing/analysis pipeline, named TaxADivA, was developed for nifH amplicons produced by Illumina paired-end sequencing, and it enables an inference of taxonomy, performs clustering, and produces output in formats that may be used by programs that facilitate data exploration and analysis. Diazotroph diversity and community composition are linked to ecosystem functioning, and our results advance the phylogenetic characterization of diazotroph communities by providing empirically derived nifH similarity cutoffs for species, genus, and family levels. The utility of our pipeline is validated for diazotroph communities in a variety of ecosystems, including contaminated beach sands, peatland ecosystems, living plant tissues, and rhizosphere soil.

Influence of genetic ancestry and socioeconomic status on type 2 diabetes in the diverse Colombian populations of Chocó and Antioquia.

Differences in genetic ancestry and socioeconomic status (SES) among Latin American populations have been linked to health disparities for a number of complex diseases, such as diabetes. We used a population genomic approach to investigate the role that genetic ancestry and socioeconomic status (SES) play in the epidemiology of type 2 diabetes (T2D) for two Colombian populations: Chocó (Afro-Latino) and Antioquia (Mestizo). Chocó has significantly higher predicted genetic risk for T2D compared to Antioquia, and the elevated predicted risk for T2D in Chocó is correlated with higher African ancestry. Despite its elevated predicted genetic risk, the population of Chocó has a three-times lower observed T2D prevalence than Antioquia, indicating that environmental factors better explain differences in T2D outcomes for Colombia. Chocó has substantially lower SES than Antioquia, suggesting that low SES in Chocó serves as a protective factor against T2D. The combination of lower prevalence of T2D and lower SES in Chocó may seem surprising given the protective nature of elevated SES in many populations in developed countries. However, low SES has also been documented to be a protective factor in rural populations in less developed countries, and this appears to be the case when comparing Chocó to Antioquia.

A Comparative Analysis of Genetic Ancestry and Admixture in the Colombian Populations of Chocó and Medellín.

At least 20% of Colombians identify as having African ancestry, yielding the second largest population of Afro-descendants in Latin America. To date, there have been relatively few studies focused on the genetic ancestry of Afro-Latino populations. We report a comparative analysis of the genetic ancestry of Chocó, a state located on Colombia's Pacific coast with a population that is >80% Afro-Colombian. We compared genome-wide patterns of genetic ancestry and admixture for Chocó to six other admixed American populations, with an emphasis on a Mestizo population from the nearby Colombian city of Medellín. One hundred sample donors from Chocó were genotyped across 610,545 genomic sites and compared with 94 publicly available whole genome sequences from Medellín. At the continental level, Chocó shows mostly African genetic ancestry (76%) with a nearly even split between European (13%) and Native American (11%) fractions, whereas Medellín has primarily European ancestry (75%), followed by Native American (18%) and African (7%). Sample donors from Chocó self-identify as having more African ancestry, and conversely less European and Native American ancestry, than can be genetically inferred, as opposed to what we previously found for Medellín, where individuals tend to overestimate levels of European ancestry. We developed a novel approach for subcontinental ancestry assignment, which allowed us to characterize subcontinental source populations for each of the three distinct continental ancestry fractions separately. Despite the clear differences between Chocó and Medellín at the level of continental ancestry, the two populations show overall patterns of subcontinental ancestry that are highly similar. Their African subcontinental ancestries are only slightly different, with Chocó showing more exclusive shared ancestry with the modern Yoruba (Nigerian) population, and Medellín having relatively more shared ancestry with West African populations in Sierra Leone and Gambia. Both populations show very similar Spanish ancestry within Europe and virtually identical patterns of Native American ancestry, with main contributions from the Embera and Waunana tribes. When the three subcontinental ancestry components are considered jointly, the populations of Chocó and Medellín are shown to be most closely related, to the exclusion of the other admixed American populations that we analyzed. We consider the implications of the existence of shared subcontinental ancestries for Colombian populations that appear, at first glance, to be clearly distinct with respect to competing notions of national identity that emphasize ethnic mixing (mestizaje) vs. group-specific identities (multiculturalism).

Comparative performance of the protocol of plasma rich in growth factors - universal 1 (PRGF-U1) for obtaining platelet rich plasma

Objective: to compare the platelet concentration obtained after application of the protocol of plasma rich in growth factors - universal 1 (PRGF-U1) and the protocol of Anitua and Andia (PRP-A) for obtaining platelet rich plasma. Material and Method: A descriptive, cross-sectional and comparative study was carried out with a simple random probabilistic sample consisting of 16 patients who attended the Periodontics service of the Unit of Second Specialization in Stomatology of the National University of Trujillo. Five blood samples were obtained from each patient, after applying a health questionnaire to rule out any disease or drug consumption, in order to obtain the baseline platelet concentration and that obtained after PRGF-U1 and PRP-A. To compare the platelet concentrations of the two protocols, Student’s t-test was used considering a significance level of p<0.05. RESULTS: The baseline platelet concentration was 371,250 +/- 68,203 platelets/ μL, for PRGF-U1 it was 747,875 +/- 121,645 platelets/μL and for PRP-A it was 595,000 +/- 129,202 platelets/ML. A statistically significant difference (p<0.001) was found between both protocols. Conclusion: The PRGF-U1 protocol yielded a higher platelet concentration compared to the Anitua and Andia protocol.