Southwest Colombia Research Articles

Frequency of Variants in DNA-Repair Genes in a Southwest Colombian Population

Abstract Objective To describe the frequency of mutations in DNA-repair genes in a southwestern Colombian population. Methods We have designed an observational study, including 162 people from all ages from southwest Colombia. We have extracted and collected their DNA in filters. We have immersed the DNA in a phosphate buffer along with DNeasy package (Thermo Fisher Scientific, Waltham, MA, USA). The preparation process was with the TruSeq Exome Library Prep (Illumina, Inc. San Diego, CA, USA), then the obtained libraries were normalized with TruSeq Rapid Exome (Illumina, Inc. San Diego, CA, USA). We sequenced the full exome and identified the variants associated with 12 genes (ataxia telangiectasia mutated [ATM], BRCA1 DNA repair associated [BRCA1], BRCA2 DNA repair associated [BRCA2], checkpoint kinase 2 [CHEK2], epithelial cell adhesion molecule [EPCAM], homeobox protein Hox-B13 [HOXB13], mutS homolog 1, 2 and 6 [MLH1, MSH2, MSH6], nibrin [NBN], PMS1 homolog 2, mismatch repair system component [PMS2], and tumor protein p53 [TP53]). Descriptive statistics were performed with the R software (The R Foundation for Statistical Computing, Vienna, Austria). Results A total of 7,315,466 pieces of data were sequenced in this population. The most frequently mutated genes were ATM (1,221 pieces of data; 13.2%), BRCA1 (1,178 pieces of data; 12.8%), BRCA2 (1,484 pieces of data; 16.12%), and NBN (965 pieces of data; 10.42%). The most common single nucleotide polymorphisms (SNPs) in these 12 genes were the following: BRCA2 (rs169547, rs206075, rs206076); ATM (rs659243, rs228589); TP53 (rs1625895, rs1042522, rs1642785); PMS2 (rs2228006, rs1805319); NBN (rs709816); and MSH6 (rs3136367) Conclusion The BRCA2, ATM, BRCA1 and NBN DNA-repair genes were the most frequently mutated in this southwestern Colombian Population.

Molecular and descriptive epidemiology of intestinal protozoan parasites of children and their pets in Cauca, Colombia: a cross-sectional study

BackgroundParasitic infections, particularly those caused by protozoa, represent a considerable public health problem in developing countries. Blastocystis, Giardia duodenalis, Cryptosporidium spp. and the Entamoeba complex (Entamoeba histolytica, Entamoeba dispar and Entamoeba moshkovskii) are the most common etiological causes of intestinal parasitic infections.MethodsWe carried out a descriptive cross-sectional study in school-age children attending a daycare institution in commune eight of Popayán, Cauca (Southwest Colombia). A total of 266 fecal samples were collected (258 from children and eight from pets). Blastocystis, G. duodenalis, Cryptosporidium spp. and the Entamoeba complex were identified by microscopy, quantitative real-time PCR (qPCR) and conventional PCR. The concordance of qPCR and microscopy was assessed using the Kappa index. Molecular characterization was conducted to identify Blastocystis subtypes (18S), G. duodenalis assemblages (tpi and gdh) and Cryptosporidium species/subtypes (18S and GP60). Potential associations between intestinal parasitism and sociodemographic factors were examined using bivariate analyses.ResultsA total of 258 fecal samples from children were analyzed by microscopy and 255 samples were analyzed by qPCR. The prevalence of Blastocystis was between 25.19% (microscopy) and 39.22% (qPCR), that of G. duodenalis was between 8.14% (microscopy) and 10.59% (qPCR), that of Cryptosporidium spp. was estimated at 9.8% (qPCR), and that of the Entamoeba complex was between 0.39% (conventional PCR) and 0.78% (microscopy). The concordance between microscopy and qPCR was very low. Blastocystis ST1 (alleles 4, 8, and 80), ST2 (alleles 11, 12, and 15), ST3 (alleles 31, 34, 36, 38,57, and 151), and ST4 (alleles 42 and 91), G. duodenalis assemblages AII, BIII, BIV and D, C. parvum subtype IIa and C. hominis subtype IbA9G3R2 were identified. The only identified member of the Entamoeba complex corresponded to E. histolytica. No statistically significant association was identified between parasitic infection and any sociodemographic variable.ConclusionThis study revealed the usefulness of molecular methods to depict the transmission dynamics of parasitic protozoa in southwest Colombia. The presence of some of these protozoa in domestic animals may be involved in their transmission.

Molecular detection and genotyping of pathogenic protozoan parasites in raw and treated water samples from southwest Colombia

BackgroundProtozoan parasites such as Giardia duodenalis, Cryptosporidium spp., Cyclospora cayetanensis, Toxoplasma gondii and Entamoeba histolytica represent a great challenge to the systems producing water for human consumption because their cystic forms are persistent in the environment and resist to the disinfection methods conventionally used for their control. In this study, we investigated the presence of these protozoan pathogens in both raw and treated water samples used for the production of drinking water in Nariño Department, southwest Colombia. We collected 110 water samples (10 lof each sample) and analyzed them with real-time PCR (qPCR). qPCR-positive samples were genotyped with PCR and DNA sequencing.ResultsGiardia duodenalis was detected in 35/110 (31.8%) of the samples and Cryptosporidium spp. in 9/110 (8.2%) of the samples; no sample was positive for T. gondii, E. histolytica or C. cayetanensis. Giardia duodenalis was detected in samples of both raw water (Drinking Water Treatment Plants (DWTP): 47.83%;Drinking Water Rural Plants (DWRP): 18.42%) and water collected either after conventional physicochemical treatment (26.09%) or after disinfection by chlorine (50%), whereas Cryptosporidium spp. were only detected in raw waters (DWTP: 17.39%; DWRP: 13.16%). The two pathogens were detected in both types of treatment plants supplying water to urban areas and to rural zones. Analysis of gdh and tpi markers identified assemblages AI, AII and H of G. duodenalis, while analysis of the small subunit rRNA and gp60 markers of Cryptosporidium-positive samples identified C. parvum (Subtype IIcA5G3c), C. galli, C. molnari, Cryptosporidium sp. genotype II of bats and Cryptosporidium sp. genotype VIII of birds.ConclusionsThe results obtained demonstrate the presence of protozoan parasites in the water of the study region, and the need to improve the surveillance systems for these pathogens and identify the corresponding sources of contamination.

Proshapalopus marimbai, a new tarantula species (Mygalomorphae, Theraphosidae) and first genus record from Colombia

A new species of Proshapalopus Mello-Leitao, 1923, distributed in the Southwest Colombia in the Choco Region, is described. A morphological cladistic analysis based on the previous matrix of a Ther...

Scaling-up biofortified beans high in iron and zinc through the school-feeding program: A sensory acceptance study with schoolchildren from two departments in southwest Colombia.

Iron and zinc deficiencies are global health problems, affecting mostly pregnant women and young children. In 2016, biofortified iron and zinc beans were introduced in Colombia. The incorporation of biofortified beans into the national school‐feeding program could facilitate adoption and potentially improve the nutritional status of large populations. However, biofortified beans have to be accepted in order to be consumed by populations. We therefore studied the sensory acceptability of two biofortified beans, BIO‐101 and BIO‐107, and local beans at schools with free feeding services in two departments of southwest Colombia. Measured on a five‐point Likert scale, the mean overall scores were 3.88 ± 0.64, 3.79 ± 0.74, and 3.81 ± 0.76, for BIO‐101, BIO‐107, and the local bean varieties, respectively, without significant differences. The children in Piendamó (Cauca) slightly preferred BIO‐107 over the local bean (p < .05) based on color, smell, and taste. The children in Caicedonia (Valle del Cauca) slightly favored the local bean over BIO‐107 (p < .05), regarding size, smell, and taste. Overall acceptability in schoolchildren was good for all beans without significant differences. This study advocates incorporation of accepted biofortified beans in the school‐feeding program, in order to reach large groups of schoolchildren and potentially improve their nutritional statuses.

Household Determinants of the Adoption of Improved Cassava Varieties using DNA Fingerprinting to Identify Varieties in Farmer Fields: A Case Study in Colombia

AbstractWe examine factors affecting the adoption of improved cassava varieties of 217 households in the Cauca Department in southwest Colombia. Using DNA fingerprinting through Single Nucleotide Polymorphisms (SNPs), we identified different cultivars in farmers fields. We also used this information to remove possible bias in the adoption model that could have resulted from a misclassification of improved varieties (IVs). As a result, we found that farmers substantially overestimate their use of IVs and there are important differences in the determinants of adoption between farmer self‐identification and DNA fingerprinting. This finding implies that the incorporation of DNA fingerprinting in IV adoption studies is important to ensure the accuracy of future agricultural economic research and the relevance of subsequent policy recommendations.

Mortalidad precoz en trasplante cardíaco

ObjectiveTo describe the main causes of mortality in the first 30 days post-heart transplant. MethodsA study was conducted on a representative patient cohort with a heart transplant performed between 2008 and 2015, and who died in the first 30 days after the procedure. The information was collected from an institutional heart transplant register. A description is presented of the sociodemographic and clinical variables, the receiver characteristics, causes of death, as well as pre-, intra-, and post-operative characteristics and complications. ResultsA total of 74 heart transplants were performed between January 2008 and August 2015. Of these, 10 patients died in the first 30 days post-transplant (a mortality rate of 13.51%). The median age was 55 years (Inter-quartile range (IQR) 26-62 years) and 50% of them were male. The median ejection fraction pre-transplant was 24% (IQR 18-47) and time on the waiting list of 81 days (IQR 12-157 days). Four of the patients were in Stage 0A, and the remaining 6 were in Stage 1. The median time between the transplant and death was 1 day (IQR 0-3 days, and the later mortality rate was at 18 days. The main causes of death were: multi-organ failure (5 cases), acute graft failure (3 cases), and peri-operative coagulopathy (2 cases). ConclusionsIn an institution of reference for heart transplantation in South-West Colombia, the early post-transplant mortality rate was 13.51%, similar to that reported in international registers. The main cause of death was multi-organ failure, which occurred mainly in the first 24hours after the heart transplant.

Chemical and nano-mineralogical study for determining potential uses of legal Colombian gold mine sludge: Experimental evidence

The present study is focused on the chemical and nano-mineralogical characterization of sludge from gold mine activities, in order to put forward diverse solution alternatives, where lack of knowledge has been found. The sample was collected from “La Estrella” mine of Suarez, located in Department of Cauca, south-west Colombia. The sludge micro-structure and chemical composition were analyzed using a high resolution transmission electron microscopy (HR-TEM) equipped with a dispersive X-ray detector (EDS). X-ray diffraction technique was employed to identify the mineralogical phases present in the sludge. Additional mineralogical characterization was done by using RAMAN spectroscopy. Main findings points to its potential to be used as a fertilizer, this is why, mine sludge contains macronutrients such as P, Ca and S, together with micronutrients like Cu. However, the presence of goethite could decrease the mobilization of nutrients to soils, thus additional alternatives, for instance, a mixture with humus or another material containing Humic Acids should be done, in order to minimizing its retention effect. Additionally, another possible uses to explore could be as construction and ceramic material or in the wastewater treatment for nutrient retention and organic material removal. Rutile (TiO2 nanoparticles) particles have been also detected, what could cause health concern due to its nanoparticle toxic character, mainly during gold extraction process.

Reference values of amino acids, acylcarnitines and succinylacetone by tandem mass spectrometry for use in newborn screening in southwest Colombia.

Introduction: Inborn errors of metabolism (IEM) represent an important public health problem due to current diagnosis and treatment limitations, poor life quality of affected patients, and consequent untimely child death. In contrast to classical methods, tandem mass spectrometry (MS/MS) has allowed simultaneous evaluation of multiple metabolites associated with IEM offering higher sensitivity, low false positive rates and high throughput.Aims: Determine concentration levels for amino acids and acylcarnitines in blood of newborns from Colombia, to establish reference values for further use in diagnosis of IEM.Methods: Implementation of a method to determine amino acids, acylcarnitines and succinylacetone in newborn dried blood spots using MS/MS, and its application in a cross-sectional study conducted in 891 healthy neonates from Cali and Quibdo cities is described. Results: fifty-seven analytes that allow the diagnosis of more than 40 different pathologies were tested. The method showed to be linear, precise and accurate. Healthy neonates 1-18 days of age were included, 523 from Cali and 368 from Quibdo; 52% male and 48% female. Age-related differences on the concentration levels of amino acids and acylcarnitines were observed whereas no significant differences by gender were found. Conclusion: The study has contributed to reveal the usual concentration levels of amino acids, acylcarnitines and succinylacetone that could be used as reference for the establishment of a newborn metabolic screening program in Colombia.

The winding ways of development: A historical journey of a road in the Putumayo region of Colombia

Roads are by nature a contested subject. Although they represent vital infrastructure to enable the flow of people, goods and ideas, their potential detrimental effects for humans and the environment have been a constant source of debate and criticism. This is particularly true for natural resource-rich regions such as the Amazon, where the development of roads has been directly associated with rampant deforestation and resource extraction, uncontrolled colonization and dispossession of indigenous lands. Yet the impact of roads goes far beyond their direct social and environmental costs and benefits. In many places of the world, roads have a strong evocative power, as they represent spaces that materially and symbolically embody ideas such as „modernity,‟ „progress,‟ „backwardness‟ and „development.‟ Combining multi-sited ethnography and historical analysis, this photo essay attempts to document the past, present, and likely future of a road in Putumayo, a region of southwest Colombia that has been traditionally considered a marginal frontier, and which has also become internationally known for the production of cocaine and the violence that has come with it. The road, as I will try to show, invites reflection about the complexities inherent to the different meanings and realities of development. Author’s Note

Correlación de la resistencia a compresión uniaxial con la humedad y porosidad eficaz en rocas

Esta investigación, consiste en la determinación del parámetro mecánico de resistencia a compresión Uniaxial en la roca y su correlación con la humedad y porosidad eficaz, propiedades físicas de la roca. Por su objetivo de estudio, el proyecto se engloba dentro del marco de la mecánica de rocas. Las rocas seleccionadas para la investigación fueron tomadas de una cantera del Sur Occidente Colombiano. La investigación condujo, a la determinación de ecuaciones que permiten estimar la resistencia a compresión Uniaxial de la roca a partir de su porosidad eficaz y del contenido de humedad. Es importante resaltar que este tipo de correlaciones son representativas para rocas que gocen de características litológicas similares a las utilizadas en la experimentación. Finalmente se presentan los resultados con sus análisis y conclusiones de la investigación.

Edge Influence on Diversity of Orchids in Andean Cloud Forests

Cloud forests harbor high levels of orchid diversity. However, due to the high fragmentation of these forests in the Andes, combined with the pressure for new agricultural land, orchid diversity is highly threatened. Despite this worrying scenario, few studies have assessed the effects of habitat loss specifically on orchid assemblages in the Andes. The aim of this study was to analyze the edge effect on orchids in cloud forest fragments of varying size. We measured forest structure, neighboring land cover and edge effect on orchid abundance, species richness and beta-diversity, by sampling assemblages along edge-to-interior transects in six different sized Andean (southwest Colombia) forest remnants. We recorded 11,127 stem-individuals of orchids in 141 species. Within the forest, edges sustained equal or more species than interior plots. Our results revealed neither patch metrics nor forest structure showed any significant association to orchid diversity at any scale. Nonetheless, from our observations in composition, the type of neighboring cover, particularly pastures, negatively influences interior species (richness and composition) in larger reserves. This might be due to the fact that some species found in interior plots tend to be confined, with sporadic appearances in regeneration forest and are very scarce or absent in pastures. Species richness differed significantly between matrix types. Our results suggest that (1) orchid diversity shows spatial variability in response to disturbances, but the response is independent from forest structure, patch size and patch geometry; (2) orchid communities are negatively affected by covers, and this pattern is reflected in reduced richness and high species turnover; (3) orchid richness edge effect across a pasture-interior gradient. Two forest management implications can be discerned from our results: (1) management strategies aiming to reduce edge effects may focus on improvement regeneration conditions around pasture lands; and (2) local scale management and conservation activities of natural forests in cloud forests will favor small reserves that harbor high levels of richness.

Effects of uncertainty on scheduling of highway construction projects

Time and cost overruns in highway construction are usual in Colombia. Contractors regularly fail in cost estimation and construction scheduling. An analysis of important factors on time and cost overruns in highway construction in southwest Colombia is presented in this paper. Forty highway construction projects were reviewed. Data from construction documents were collected to prepare a data base for probabilistic analysis. Data collected include scheduled construction time and cost, actual construction time and cost, and unexpected events which could have affected the construction process. Data were used in a probabilistic cost and schedule risk analysis to identify critical factors in construction time and cost overruns in the region. It was found that the activities that most affect the time and cost overruns are the construction of the granular base and the asphalt layer. The most common causes of construction overruns were found to be poor cost and duration estimates, rain, and materials supply problems.

Projected impact of twenty-first century ENSO changes on rainfall over Central America and northwest South America from CMIP5 AOGCMs

Due to the importance that the El Nino-Southern Oscillation (ENSO) has on rainfall over the tropical Americas, future changes in ENSO characteristics and teleconnections are important for regional hydroclimate. Projected changes to the ENSO mean state and characteristics, and the resulting impacts on rainfall anomalies over Central America, Colombia, and Ecuador during the twenty-first century are explored for several forcing scenarios using a suite of coupled atmosphere–ocean global climate models (AOGCMs) from the fifth phase of the Coupled Model Intercomparison Project (CMIP5). Mean-state warming of eastern tropical Pacific sea surface temperatures, drying of Central America and northern Colombia, and wetting of southwest Colombia and Ecuador are consistent with previous studies that used earlier versions of the AOGCMs. Current and projected future characteristics of ENSO (frequency, duration, amplitude) show a wide range of values across the various AOGCMs. The magnitude of ENSO-related rainfall anomalies are currently underestimated by most of the models, but the model ensembles generally simulate the correct sign of the anomalies across the seasons around the peak ENSO effects. While the models capture the broad present-day ENSO-related rainfall anomalies, there is not a clear sense of projected future changes in the precipitation anomalies.

Participación política de los indígenas del Cauca como construcción de ciudadanía

Este artículo trata sobre la problemática de la participación política de los grupos indígenas en el suroccidente colombiano, haciendo principal referencia a las comunidades del norte del Cauca, teniendo como marco principal el municipio de Toribio. En este sentido, la participación indígena es analizada desde diferentes elementos abordados como: las dimensiones histórico-culturales, políticas y económicas que los motivaron a realizar una movilización colectiva, un diagnóstico del conflicto armado, y el modelo de cabildo urbano en Santiago de Cali, así como sus procesos de consolidación y construcción de paz desde la participación local. Con ello se busca elaborar unas conclusiones básicas para una mayor compresión de las dinámicas políticosociales de esas comunidades.

El sentido de lo comunitario: tensiones entre el liberalismo y comunitarismo en territorios locales del Cauca, Colombia

The purpose of the research was to identify the aspects influencing the environmental history of solidarity and strengthening processes of local and regional identities in rural areas in southwest Colombia. The methodology was based on the design and the carrying out of itinerant workshops of Participatory Rural Development, Ethnographic records and semistructured interviews. The results highlight the ethical and political tensions in the department of Cauca between liberalism and communitarianism which become central issues in the definition of the sense of community in rural, indigenous and Afro-descendant population.

Endophytic fungi associated with natural populations of &lt;i&gt;Vanilla&lt;/i&gt; species in south-west Colombia

Endophytic fungi associated with natural populations of &lt;i&gt;Vanilla&lt;/i&gt; species in south-west Colombia

Spatial pattern recognition of seismic events in South West Colombia

Recognition of seismogenic zones in geographical regions supports seismic hazard studies. This recognition is usually based on visual, qualitative and subjective analysis of data. Spatial pattern recognition provides a well founded means to obtain relevant information from large amounts of data. The purpose of this work is to identify and classify spatial patterns in instrumental data of the South West Colombian seismic database. In this research, clustering tendency analysis validates whether seismic database possesses a clustering structure. A non-supervised fuzzy clustering algorithm creates groups of seismic events. Given the sensitivity of fuzzy clustering algorithms to centroid initial positions, we proposed a methodology to initialize centroids that generates stable partitions with respect to centroid initialization. As a result of this work, a public software tool provides the user with the routines developed for clustering methodology. The analysis of the seismogenic zones obtained reveals meaningful spatial patterns in South-West Colombia. The clustering analysis provides a quantitative location and dispersion of seismogenic zones that facilitates seismological interpretations of seismic activities in South West Colombia.

Microbiological characteristics of kumis, a traditional fermented Colombian milk, with particular emphasis on enterococci population

Kumis is a traditional fermented cow milk produced and consumed in South West Colombia. The main objective of this research was to studied the enterococcal population, present in 13 kumis samples traditionally manufactured, for their role as beneficial organisms or opportunistic pathogens. The molecular identification of 72 isolates evidenced that Enterococcus faecalis and E. faecium were the dominant species. The genes gelE, esp, asa1, cyl and hyl, all associated with virulence factors in enterococci, were detected in 30 isolates, while 42 were free of virulence determinants. Skim milk media were fermented by all the different isolates and further tested for proteolysis (free NH 3 groups), Angiotensin-I Converting Enzyme (ACE) inhibitory activity and biogenic amines production. Nine E. faecalis and two E. faecium strains produced fermented milk with ACE-inhibitory activity values ranging from 39.7% to 84.35% .The digestion of fermented milk samples by pepsin and pancreatin evidenced an increase in ACE inhibitory activity, with E. faecalis KE09 as the best producer (IC50 = 14.25 μg ml −1). Moreover, the strains showed a very low tyrosine decarboxylase activity and did not produce histamine during 48 h fermentation in milk. This study underlines the that Colombian kumis is a good source of not virulent enterococci able to produce fermented milks with ACE-inhibitory activity.

Genetic diversity and population structure of the Guinea pig (Cavia porcellus, Rodentia, caviidae) in Colombia

The aim was to establish the genetic diversity and population structure of three guinea pig lines, from seven production zones located in Nariño, southwest Colombia. A total of 384 individuals were genotyped with six microsatellite markers. The measurement of intrapopulation diversity revealed allelic richness ranging from 3.0 to 6.56, and observed heterozygosity (Ho) from 0.33 to 0.60, with a deficit in heterozygous individuals. Although statistically significant (p < 0.05), genetic differentiation between population pairs was found to be low. Genetic distance, as well as clustering of guinea-pig lines and populations, coincided with the historical and geographical distribution of the populations. Likewise, high genetic identity between improved and native lines was established. An analysis of group probabilistic assignment revealed that each line should not be considered as a genetically homogeneous group. The findings corroborate the absorption of native genetic material into the improved line introduced into Colombia from Peru. It is necessary to establish conservation programs for native-line individuals in Nariño, and control genealogical and production records in order to reduce the inbreeding values in the populations.