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Ítem Extracted information quality, a comparative study in high and low dimensions(Inderscience Enterprises Ltd., 2020-12-11) Ariza-Jimenez L.; Villa, LF; Pinel N.; Lucia Quintero M, O.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónÍtem Identification of Fusarium cf . verticillioides as The Causal Agent of Pokka Boheng Disease in Sugarcane in the Department of Antioquia, Colombia(Fondo Editorial Universidad EAFIT, 2018-11-01) Franco, Nicolas David; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónÍtem Implementation of a Non-InvasiveBioprospecting Protocol for Isolation ofLactobacillusfrom Feces of Hens UnderForaging Conditions(Fondo Editorial Universidad EAFIT, 2018-07-01) Correa, Javier; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónÍtem Identification of Fusarium cf. Verticillioides as The Causal Agent of Pokka Boheng Disease in Sugarcane in the Department of Antioquia, Colombia(Fondo Editorial Universidad EAFIT, 2018-07-01) Correa, Javier; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónÍtem Rol de la función mitocondrial en el corazón y sus implicaciones en disfunciones cardíacas(Fondo Editorial Universidad EAFIT, 2017-11-01) Franco, Nicolas David; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónÍtem A revision of the didelphid marsupial genus Marmosops part 1. Species of the subgenus Sciophanes.(AMER MUSEUM NATURAL HISTORY, 2016-05-01) Diaz, Juan Fernando; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónÍtem Revisión de las localidades fosilíferas del departamento de Antioquia, Colombia(Geological Engineering Curriculum Program, Geosciences and Environment College of Mines Faculty, National University of Colombia - Medellin Headquarters, 2016-08-01) Cardenas, Andres Leonardo; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónÍtem An Entropy-Based Graph Construction Method for Representing and Clustering Biological Data(SPRINGER, 2019-10-01) Ariza-Jiménez L.; Pinel N.; Villa L.F.; Quintero O.L.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónUnsupervised learning methods are commonly used to perform the non-trivial task of uncovering structure in biological data. However, conventional approaches rely on methods that make assumptions about data distribution and reduce the dimensionality of the input data. Here we propose the incorporation of entropy related measures into the process of constructing graph-based representations for biological datasets in order to uncover their inner structure. Experimental results demonstrated the potential of the proposed entropy-based graph data representation to cope with biological applications related to unsupervised learning problems, such as metagenomic binning and neuronal spike sorting, in which it is necessary to organize data into unknown and meaningful groups. © 2020, Springer Nature Switzerland AG.Ítem Unravelling the widening of the earliest Andean northern orogen: Maastrichtian to early Eocene intra-basinal deformation in the northern Eastern Cordillera of Colombia(Wiley-Blackwell Publishing Ltd, 2020-07-21) Bayona G.; Baquero M.; Ramírez C.; Tabares M.; Salazar A.M.; Nova G.; Duarte E.; Pardo A.; Plata A.; Jaramillo C.; Rodríguez G.; Caballero V.; Cardona A.; Montes C.; Gómez Marulanda S.; Cárdenas-Rozo A.L.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónThe onset of deformation in the northern Andes is overprinted by subsequent stages of basin deformation, complicating the examination of competing models illustrating potential location of earliest synorogenic basins and uplifts. To establish the width of the earliest northern Andean orogen, we carried out field mapping, palynological dating, sedimentary, stratigraphic and provenance analyses in Campanian to lower Eocene units exposed in the northern Eastern Cordillera of Colombia (Cocuy region) and compare the results with coeval succession in adjacent basins. The onset of deformation is recorded in earliest Maastrichtian time, as terrigenous detritus arrived into the basin marking the end of chemical precipitation and the onset of clastic deposition produced by the uplift of a western source area dominated by shaly Cretaceous rocks. Disconformable contacts within the upper Maastrichtian to middle Palaeocene succession document increasing supply of quartzose sandy detritus from Cretaceous quartzose rocks exposed in eastern source areas. The continued unroofing of both source areas produced a rapid shift in depositional environments from shallow marine in Maastrichtian to fluvial-lacustrine systems during the Palaeocene-early Eocene. Supply of immature Jurassic sandstones from nearby western uplifts, together with localized plutonic and volcanic Cretaceous rocks, caused a shift in Palaeocene sandstones composition from quartzarenites to litharenites. Supply of detrital sandy fragments, unstable heavy minerals and Cretaceous to Ordovician detrital zircons, were derived from nearby uplifted blocks and from SW fluvial systems within the synorogenic basin, instead of distal basement rocks. The presence of volcanic rock fragments and 51–59 Ma volcanic zircons constrain magmatism within the basin. The Maastrichtian–Palaeocene sequence studied here documents crustal deformation that correlates with coeval deformation farther south in Ecuador and Peru. Slab flattening of the subducting Caribbean plate produced a wider orogen (>400 km) with a continental magmatic arc and intra-basinal deformation and magmatism. © 2020 International Association of Sedimentologists and European Association of Geoscientists and Engineers and John Wiley - Sons LtdÍtem Efficient direct shoot organogenesis and genetic stability in micropropagated sacha inchi (Plukenetia volubilis L.)(BioMed Central Ltd., 2020-09-03) Restrepo-Osorio C.; Gil-Correal A.; Chamorro-Gutiérrez L.; Ramírez-Ríos V.; Álvarez J.C.; Villanueva-Mejía D.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónObjective: It is necessary to improve biotech platforms based on in vitro cell tissue culture to support sacha inchi (Plukenetia volubilis L.) research programs and draw on the nutritional value of the high polyunsaturated fatty acid content of its oilseed. Here, we developed a rapid and efficient method for induction and direct in vitro shoot development for this species. Results: Shoots were generated from hypocotyl explants. The highest organogenic response was obtained in woody plant medium supplemented with 1 mg/L thidiazuron and 0.5 mg/L zeatin supplemented with L-glutamine, adenine hemisulfate, and L-arginine. Shoots obtained using this medium were transferred and subcultivated with different concentrations of indole-3-butyric acid and 1-naphthylacetic acid for rooting. For the first time, a histological analysis was performed supporting direct organogenic development in this species. The plantlets obtained were transferred ex vitro with a survival percentage of 80%. The genetic stability of the plants recovered was confirmed by randomly amplified polymorphic DNA analysis. All results indicate that it would be possible to stimulate direct shoot formation from hypocotyls to support the sustainable use of this species. © 2020 The Author(s).Ítem Molecular and morphological identification of Phylloderma stenops Peters, 1865 (Chiroptera, Phyllostomidae) and new records for Colombia(Centro de Referencia em Informacao Ambiental, 2019-01-01) Martínez-Cerón J.M.; Patiño-Castillo E.; Carvalho-Madrigal S.; Díaz-Nieto J.F.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónBased on revisionary work of recently collected material in Colombian museums we confirm the presence of Phylloderma stenops Peters, 1865 in 6 new localities for the country, including the first record of the species in the dry lowlands of the northern Caribbean coast, and the increase by more than 800 m of the elevational range of the species in Colombia. DNA-barcoding confirmed our morphological identification, and supported a paraphyletic composition of the cis-Andean populations. Our records exemplify the little knowledge on the ecogeographic distribution of this species and provide further evidence to consider this as a widespread but rare species. © Martínez-Cerón et al.Ítem A REVISION OF THE DIDELPHID MARSUPIAL GENUS MARMOSA PART 2. SPECIES OF THE RAPPOSA GROUP (SUBGENUS MICOUREUS)(AMER MUSEUM NATURAL HISTORY, 2020-06-01) Voss, Robert S.; Giarla, Thomas C.; Diaz-Nieto, Juan F.; Jansa, Sharon A.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónIn this report, the second of a revisionary series on mouse opossums (Marmosa), we analyze cytochrome b sequence data from 166 specimens of the subgenus Micoureus and delimit putative species using the multirate Poisson Tree Processes (mPTP) method. That analysis identifies 21 putative species, many of which can be matched with available names, including alstoni, constantiae, demerarae, limae, germana, meridae, paraguayana, parda, perplexa, phaea, rapposa, and rutteri. However, some of these nominal taxa are not morphologically diagnosable, and in the absence of other corroborating evidence, we do not recommend that they all be recognized as valid. Phylogenetic analyses of a multigene dataset suggest that putative species of Micoureus belong to several wellsupported clades, one of which (the ``Rapposa Group'') is revised in this report. As defined herein, the Rapposa Group includes at least three valid species: M. rapposa Thomas, 1899 (including budini Thomas, 1920); M. parda Tate, 1931; and M. rutteri Thomas, 1924. Herein we document their ecogeographic distributions and diagnostic traits, comment on their taxonomic histories, and list the specimens we examined (including all relevant type material).Ítem A Revision of the Didelphid Marsupial Genus MarmosaPart 2. Species of the Rapposa Group (Subgenus Micoureus)(AMER MUSEUM NATURAL HISTORY, 2020-01-01) Voss, R.S.; Giarla, T.C.; Diáz-Nieto, J.F.; Jansa, S.A.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónIn this report, the second of a revisionary series on mouse opossums (Marmosa), we analyze cytochrome b sequence data from 166 specimens of the subgenus Micoureus and delimit putative species using the multirate Poisson Tree Processes (mPTP) method. That analysis identifies 21 putative species, many of which can be matched with available names, including alstoni, constantiae, demerarae, limae, germana, meridae, paraguayana, parda, perplexa, phaea, rapposa, and rutteri. However, some of these nominal taxa are not morphologically diagnosable, and in the absence of other corroborating evidence, we do not recommend that they all be recognized as valid. Phylogenetic analyses of a multigene dataset suggest that putative species of Micoureus belong to several well-supported clades, one of which (the "Rapposa Group") is revised in this report. As defined herein, the Rapposa Group includes at least three valid species: M. rapposa Thomas, 1899 (including budini Thomas, 1920); M. pardaTate, 1931; and M. rutteriThomas, 1924. Herein we document their ecogeographic distributions and diagnostic traits, comment on their taxonomic histories, and list the specimens we examined (including all relevant type material). © 2020 American Museum of Natural History.Ítem Rapid mitochondrial genome sequencing based on Oxford Nanopore Sequencing and a proxy for vertebrate species identification(John Wiley and Sons Ltd, 2020-01-01) Franco-Sierra, N.D.; Díaz-Nieto, J.F.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónMolecular information is crucial for species identification when facing challenging morphology-based specimen identifications. The use of DNA barcodes partially solves this problem, but in some cases when PCR is not an option (i.e., primers are not available, problems in reaction standardization), amplification-free approaches could be an optimal alternative. Recent advances in DNA sequencing, like the MinION device from Oxford Nanopore Technologies (ONT), allow to obtain genomic data with low laboratory and technical requirements, and at a relatively low cost. In this study, we explore ONT sequencing for molecular species identification from a total DNA sample obtained from a neotropical rodent and we also test the technology for complete mitochondrial genome reconstruction via genome skimming. We were able to obtain “de novo” the complete mitogenome of a specimen from the genus Melanomys (Cricetidae: Sigmodontinae) with average depth coverage of 78X using ONT-only data and by combining multiple assembly routines. Our pipeline for an automated species identification was able to identify the sample using unassembled sequence data (raw) in a reasonable computing time, which was substantially reduced when a priori information related to the organism identity was known. Our findings suggest ONT sequencing as a suitable candidate to solve species identification problems in metazoan nonmodel organisms and generate complete mtDNA datasets. © 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.Ítem Bacillus subtilis EA-CB0575 genome reveals clues for plant growth promotion and potential for sustainable agriculture(Springer, 2020-01-01) Franco-Sierra, N.D.; Posada, L.F.; Santa-María, G.; Romero-Tabarez, M.; Villegas-Escobar, V.; Álvarez, J.C.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónBacillus subtilis is a remarkably diverse bacterial species that displays many ecological functions. Given its genomic diversity, the strain Bacillus subtilis EA-CB0575, isolated from the rhizosphere of a banana plant, was sequenced and assembled to determine the genomic potential associated with its plant growth promotion potential. The genome was sequenced by Illumina technology and assembled using Velvet 1.2.10, resulting in a whole genome of 4.09 Mb with 4332 genes. Genes involved in the production of indoles, siderophores, lipopeptides, volatile compounds, phytase, bacilibactin, and nitrogenase were predicted by gene annotation or by metabolic pathway prediction by RAST. These potential traits were determined using in vitro biochemical tests, finding that B. subtilis EA-CB0575 produces two families of lipopeptides (surfactin and fengycin), solubilizes phosphate, fixes nitrogen, and produces indole and siderophores compounds. Finally, strain EA-CB0575 increased 34.60% the total dry weight (TDW) of tomato plants with respect to non-inoculated plants at greenhouse level. These results suggest that the identification of strain-specific genes and predicted metabolic pathways might explain the strain potential to promote plant growth by several mechanisms of action, accelerating the development of plant biostimulants for sustainable agricultural. © 2020, Springer-Verlag GmbH Germany, part of Springer Nature.Ítem Forecasting PM10 and PM2.5 in the Aburrá Valley (Medellín, Colombia) via EnKF based data assimilation(Elsevier Ltd., 2020-07-10) Quintero, O.; López, S.; Yarce, A.; Pinel, N.; Segers, Arjo; Heemink, A.W; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónÍtem New insights into Late Devonian vertebrates and associated fauna from the Cuche Formation (Floresta Massif, Colombia)(Taylor & Francis, 2019-01-01) Olive, Sebastien; Pradel, Alan; Martinez-Perez, Carlos; Janvier, Philippe; Lamsdell, James C.; Gueriau, Pierre; Rabet, Nicolas; Duranleau-Gagnon, Philippe; Cardenas-Rozo, Andres L.; Zapata Ramirez, Paula A.; Botella, Hector; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónNew vertebrate remains are reported from the Late Devonian (?Frasnian) Cuche Formation of northeastern Colombia, including a new taxon of antiarch placoderm (Colombialepis villarroeli, gen. et sp. nov., previously reported as Asterolepis) and a new taxon of arthrodiran placoderm (Colombiaspis rinconensis, gen. et sp. nov.). We also report evidence of a stegotrachelid actinopterygian, a diplacanthid acanthodian (cf. Florestacanthus morenoi), a second antiarch placoderm (Bothriolepis sp.), a putative megalichthyid, and a putative tristichopterid. The absence of typical Euramerican markers, e.g., Asterolepis and Strepsodus, in this assemblage suggests that faunal interchange between Euramerica and Gondwana was less pronounced during the Frasnian-Famennian than previously thought (i.e., the Great Devonian Interchange hypothesis). Three arthropod taxa, including two families of spinicaudatan branchiopods and the eurypterid Pterygotus cf. bolivianus, are found to be associated with the reported vertebrate fauna. Pterygotus cf. bolivianus represents the first eurypterid described from Colombia and the youngest known pterygotid eurypterid, highlighting that pterygotids, which were competitors for large predatory fishes, did not go extinct during the major vertebrate radiation in the Early and Middle Devonian.Ítem Colombia's cyberinfrastructure for biodiversity: Building data infrastructure in emerging countries to foster socioeconomic growth(Wiley Open Access, 2019-12-22) De Vega, Jose J.; Davey, Robert P.; Duitama, Jorge; Escobar, Dairo; Cristancho, Marco A.; Etherington, Graham J.; Minotto, Alice; Pineda J.D.; Correa Alvarez J; Camargo, Anyela V.; Haerty, Wilfried; Mallarino, Juan P.; Barreto, Emiliano; Fuentes, Narcis; Di, Federica; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónScience and innovation are not a luxury but a prerequisite for social and economic development (Annan, 2003).Ítem Inducible Antibacterial Activity in the Bacillales by Triphenyl Tetrazolium Chloride(Nature Publishing Group, 2020-01-01) Sierra-Zapata L.; Álvarez J.C.; Romero-Tabarez M.; Silby M.W.; Traxler M.F.; Behie S.W.; Pessotti R.C.; Villegas-Escobar V.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónThe world is in the midst of an antimicrobial resistance crisis, driving a need to discover novel antibiotic substances. Using chemical cues as inducers to unveil a microorganism’s full metabolic potential is considered a successful strategy. To this end, we investigated an inducible antagonistic behavior in multiple isolates of the order Bacillales, where large inhibition zones were produced against Ralstonia solanacearum only when grown in the presence of the indicator triphenyl tetrazolium chloride (TTC). This bioactivity was produced in a TTC-dose dependent manner. Escherichia coli and Staphylococcus sp. isolates were also inhibited by Bacillus sp. strains in TTC presence, to a lesser extent. Knockout mutants and transcriptomic analysis of B. subtilis NCIB 3610 cells revealed that genes from the L-histidine biosynthetic pathway, the purine, pyrimidine de novo synthesis and salvage and interconversion routes, were significantly upregulated. Chemical space studied through metabolomic analysis, showed increased presence of nitrogenous compounds in extracts from induced bacteria. The metabolites orotic acid and L-phenylalaninamide were tested against R. solanacearum, E. coli, Staphylococcus sp. and B. subtilis, and exhibited activity against pathogens only in the presence of TTC, suggesting a biotransformation of nitrogenous compounds in Bacillus sp. cells as the plausible cause of the inducible antagonistic behavior. © 2020, The Author(s).Ítem Mercury levels in birds and small rodents from Las Orquideas National Natural Park, Colombia(Springer Verlag, 2018-12-01) Sierra-Marquez L.; Peñuela-Gomez S.; Franco-Espinosa L.; Gomez-Ruiz D.; Diaz-Nieto J.; Sierra-Marquez J.; Olivero-Verbel J.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y ConservaciónMercury (Hg) is a heavy metal known as one of the most toxic elements on the planet. The importance of Hg on living organisms resides on its biomagnification ability. Artisanal gold extraction activities release substantial amounts of this metal, polluting the ecosystems. To assess the impact of gold mining in Las Orquideas National Natural Park (Colombia), total Hg (T-Hg) levels were evaluated from 37 bird and 8 small rodent species collected at two sites within the boundaries of the Natural Park (Abriaqui and Frontino municipalities) that have experienced some gold-extraction history. The mean concentration of T-Hg in bird feathers from both sites was 0.84 ± 0.05 µg/g fw. Differences between species were found according to diet. Total Hg levels were greater on insectivorous (1.00 ± 0.08 µg/g fw), followed by nectarivorous (0.73 ± 0.07 µg/g fw) and frugivorus (0.57 ± 0.09 µg/g fw) species. These Hg levels were greater than those found in feathers from a control sample belonging to the species Penelope perspicax (0.53 ± 0.03 µg/g fw), a frugivorous species living at the Otun Quimbaya Fauna and Flora Sanctuary, a forest without known gold mining. Mercury concentrations in the livers of small rodents were greater in specimens from Frontino (0.15 ± 0.01 µg/g fw) than those from Abriaqui (0.11 ± 0.01 µg/g fw), but levels were not different between species. These results indicate that Hg in birds depends mainly on their diet, but geographical location may affect Hg concentration in rodents. Moreover, Hg sources in natural parks of Colombia may not rely solely on gold mining, atmospheric deposition, among others factors, could be influencing its accumulation in biota. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature.