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Ítem Technological surveillance as a tool for guidance research polygalacturonases processing of fruits and vegetables(Universidad Nacional De Colombia, 2014-06-01) GIRALDO, CATALINA; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)Ítem 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; Ciencias Biológicas y Bioprocesos (CIBIOP)Ítem Biodegradation of vegetable residues by polygalacturonase-agar using a trickle-bed bioreactor. En: Food and Bioproducts Processing(Institution of Chemical Engineers, 2018-09-01) GIRALDO, CATALINA; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)Ítem ReDU: a framework to find and reanalyze public mass spectrometry data(Nature Publishing Group, 2020-01-01) Jarmusch A.K.; Wang M.; Aceves C.M.; Advani R.S.; Aguirre S.; Aksenov A.A.; Aleti G.; Aron A.T.; Bauermeister A.; Bolleddu S.; Bouslimani A.; Caraballo Rodriguez A.M.; Chaar R.; Coras R.; Elijah E.O.; Ernst M.; Gauglitz J.M.; Gentry E.C.; Husband M.; Jarmusch S.A.; Jones K.L.; II; Kamenik Z.; Le Gouellec A.; Lu A.; McCall L.-I.; McPhail K.L.; Meehan M.J.; Melnik A.V.; Menezes R.C.; Montoya Giraldo Y.A.; Nguyen N.H.; Nothias L.F.; Nothias-Esposito M.; Panitchpakdi M.; Petras D.; Quinn R.A.; Sikora N.; van der Hooft J.J.J.; Vargas F.; Vrbanac A.; Weldon K.C.; Knight R.; Bandeira N.; Dorrestein P.C.; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)We present ReDU (https://redu.ucsd.edu/), a system for metadata capture of public mass spectrometry-based metabolomics data, with validated controlled vocabularies. Systematic capture of knowledge enables the reanalysis of public data and/or co-analysis of one’s own data. ReDU enables multiple types of analyses, including finding chemicals and associated metadata, comparing the shared and different chemicals between groups of samples, and metadata-filtered, repository-scale molecular networking. © 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.Ítem 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; Ciencias Biológicas y Bioprocesos (CIBIOP)Ítem 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; Ciencias Biológicas y Bioprocesos (CIBIOP)Objective: 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 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; Ciencias Biológicas y Bioprocesos (CIBIOP)Bacillus 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 Estudio fitoquímico y evaluación de la actividad antioxidante de Esenbeckia litoralis Donn.Sm. (Loro grande)(Editorial Ciencias Medicas, 2016-10-01) SAEZ, ALEX ARMANDO; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)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; Ciencias Biológicas y Bioprocesos (CIBIOP)Ítem Colombia's cyberinfrastructure for biodiversity: Building data infrastructure in emerging countries to foster socioeconomic growth(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; Ciencias Biológicas y Bioprocesos (CIBIOP)Science and innovation are not a luxury but a prerequisite for social and economic development (Annan, 2003).Ítem Complete mitogenome of the biocontroller fungus Purpureocillium sp. (Ascomycota, Ophiocordycipitaceae, Hypocreales)(Taylor and Francis Ltd., 2018-01-01) Cardona N.L.; Franco-Sierra N.D.; Correa Alvarez J.; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)The strain Purpureocillium sp. UdeA0106 is an antagonist of nematodes, fungi, and garden symphylans from crops with high economic importance in Colombia (Salazar 2013; Salazar et al. 2014; Cardona et al. 2014; Gallego et al. 2014) and is being studied to be proposed as new species. It was included on the 1000 fungal genomes project to elucidate its phylogenetic relationships with other fungi. Purpureocillium’s mitogenome has 23,495 bp of circular size. It contains 15 protein-coding genes without duplications (PCGs), corresponding to the 60% of its total length, 23 transfer genes (7.6% tRNA), two of them duplicated (trnR and trnM), and two ribosomal genes (17.6% rRNA) and a GC content of 28.44%. A phylogenetic tree was proposed using their 14 PCGs mitochondrial genes and was compared with other fungi of the Subphylum Pezizomycotina. Phylogenetics relationships showed UdeA0106 to be close to P. chlamydosporia and M. anisopliae forming a cluster with other fungal biocontrol agents and separated the strain of plant pathogenic fungi. © 2018, © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.Ítem DIRECT in vitro REGENERATION OF CASTOR BEAN PLANTS (Ricinus communis) USING EPICOTYLS(Univ Feder Uberlandia, 2019-03-15) D.F. Villanueva-Mejía; Álvarez, J.C.; Gil, Alejandro; Restrepo, Martha Catalina; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)regeneration protocol for castor bean plant (Ricinus communis) was successfully developed using epicotyl sections obtained from in vitro seedlings.Ítem New stable phases of glycine crystals(Elsevier BV, 2020-02-01) Guerra, Doris; Gomez, Luis A.; Restrepo, Albeiro; David, Jorge; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)A Density Functional Theory (DFT) study of the electronic, energetic, dynamical, and mechanical properties of new glycine molecular crystals is presented here. Our search of the potential energy surface (PES) reproduces the previously reported structures for alpha-, beta-, and gamma-glycine with P2(1/n), P2(1), P3(1) symmetries, respectively. In addition, we report three new orthorhombic (o), tetragonal (t), and monoclinic (m) crystals with P2(1)2(1)2(1), P4(3), and P2(1) symmetries. The crystals have wide band gaps, classifying them in the range of insulators. All three new phases have low mechanical hardness (< 3.2 GPa), characterizing them as soft crystals. Topological and local energetic properties of the electronic densities for the new crystalline phases of glycine have been calculated using the tools provided by the quantum theory of atoms in molecules (QTAIM) under periodic conditions. Typical NH center dot center dot center dot O, OH center dot center dot center dot O as well as secondary CH center dot center dot center dot O hydrogen bonds (HBs), act as the stabilizing factors resulting in large cohesive energies for the new phases of glycine crystals. Without exception, all types of HBs, for all new phases, perfectly fit the attractive region of a Lennard-Jones potential.Ítem 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; Ciencias Biológicas y Bioprocesos (CIBIOP)Unsupervised 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 Efecto de las Bajas Concentraciones de Nitratos y Fosfatos sobre la Acumulación de Astaxantina en Haematococcus pluvialis UTEX 2505(Centro de Informacion Tecnologica, 2019-01-01) Miranda A.M.; Ossa E.A.; Vargas G.J.; Sáez A.A.; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)In this study, the effect of the concentration of nitrogen and phosphorus on the accumulation of Astaxanthin in Haematococcus pluvialis UTEX 2505 was evaluated using a factorial 3 2 design. The dependent variables were cell growth, Astaxanthin production, lipid profile and Young's modulus of the cell membrane. It was found that cellular productivity increases when nitrogen levels were high, in contrast to low concentrations of nitrogen and phosphorus that showed a positive effect on Astaxanthin production. The stress generated by the source of nutrients decreases the rigidity of the cellular wall in the microalgae. As a conclusion, to obtain higher concentrations of Astaxanthin it is necessary to limit the nitrogen and phosphorus levels. © 2019 Centro de Informacion Tecnologica. All Rights Reserved.Ítem Volumetric power input as a reliable parameter for scale-up from shake flask to stirred-tank bioreactor: Production of a recombinant glycoprotein by Streptomyces lividans(Universidad Autonoma Metropolitana-Iztapalapa, 2019-01-01) Gamboa-Suasnavart R.A.; Marín-Palacio L.D.; López-Griego L.; Córdova-Aguilar M.S.; Valdez-Cruz N.A.; Trujillo-Roldán M.A.; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)The filamentous morphology of Streptomyces lividans depends on the culture conditions, affecting the production, secretion and post-translational modifications of recombinant glycoproteins. In this work, the previously reported volumetric power input (P/V) in conventional (NF) and coiled (CF) shake flasks were scaled-up to a stirred bioreactor. The effects on the growth and morphology of S. lividans were analyzed, as well as, the production and O-mannosylation of the recombinant APA glycoprotein from Mycobacterium tuberculosis. Specific growth rates of 5. lividans and similar recombinant glycoprotein (rAPA) yields were observed between NF and bioreactor cultures. In addition, we have found up to seven mannose residues attached to the C-terminal of the rAPA in bioreactor cultures, one more than in NF and CF. However, at similar P/V values, morphological and kinetic differences were found. Our data indicate that P/V as scale-up criteria in the production of recombinant glycoproteins in S. lividans can be successful in some, but not all the kinetic and stoichiometric parameters, suggesting that the metabolic cell responses can be affected by aeration/hydrodynamics between bioreactor and shake flasks. © 2019, Universidad Autonoma Metropolitana Iztapalapa. All rights reserved.Ítem Modern Biotechnology for Agricultural Development in Colombia(Fondo Editorial Universidad EAFIT, 2018-11-23) Villanueva, D.; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)Ítem Unsupervised fuzzy binning of metagenomic sequence fragments on three-dimensional Barnes-Hut t-Stochastic Neighbor Embeddings(Institute of Electrical and Electronics Engineers Inc., 2018-01-01) Ariza-Jimenez L.; Quintero O.L.; Pinel N.; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)Shotgun metagenomic studies attempt to reconstruct population genome sequences from complex microbial communities. In some traditional genome demarcation approaches, high-dimensional sequence data are embedded into two-dimensional spaces and subsequently binned into candidate genomic populations. One such approach uses a combination of the Barnes-Hut approximation and the t -Stochastic Neighbor Embedding (BH-SNE) algorithm for dimensionality reduction of DNA sequence data pentamer profiles; and demarcation of groups based on Gaussian mixture models within humanimposed boundaries. We found that genome demarcation from three-dimensional BH-SNE embeddings consistently results in more accurate binnings than 2-D embeddings. We further addressed the lack of a priori population number information by developing an unsupervised binning approach based on the Subtractive and Fuzzy c-means (FCM) clustering algorithms combined with internal clustering validity indices. Lastly, we addressed the subject of shared membership of individual data objects in a mixed community by assigning a degree of membership to individual objects using the FCM algorithm, and discriminated between confidently binned and uncertain sequence data objects from the community for subsequent biological interpretation. The binning of metagenome sequence fragments according to thresholds in the degree of membership opens the door for the identification of horizontally transferred elements and other genomic regions of uncertain assignment in which biologically meaningful information resides. The reported approach improves the unsupervised genome demarcation of populations within complex communities, increases the confidence in the coherence of the binned elements, and enables the identification of evolutionary processes ignored in hard-binning approaches in shotgun metagenomic studies. © 2018 IEEE.Ítem Phylogenetic and pathogenic variability of strains of Ralstonia solanacearum causing moko disease in Colombia(Blackwell Publishing Inc., 2020-02-01) Ramirez, M.; Moncada, R. N.; Villegas-Escobar, V.; Jackson, R. W.; Ramirez, C. A.; Universidad EAFIT. Departamento de Ciencias; Ciencias Biológicas y Bioprocesos (CIBIOP)Moko disease, caused by the bacterium Ralstonia solanacearum, is one of the most devastating diseases of Musa spp. in Colombia, where banana and plantain are major crops. The disease epidemiology is poorly understood and little is known about the diversity of the bacterial populations associated with this disease. This study assessed the diversity, phylogenetic relationship and pathogenicity of R. solanacearum strains associated with moko disease in Colombia. For this, the genetic diversity of 65 isolates obtained from four banana/plantain-growing regions was evaluated by using multiplex PCR and analysing the partial sequences of the mutS, rplB and egl genes. These analyses revealed that all the strains belonged to the R. solanacearum phylotype II, sequevars 4 and 6. In addition, the phylogenetic analysis assorted the strains into three subgroups, which matched the region of isolation: (i) central region (i.e. Eastern plains and Andes, IIB/4); (ii) northwest (i.e. Uraba and a few strains from Magdalena, IIB/4); and (iii) north coast (Magdalena and a few strains from Uraba, IIA/6). In addition, this evolutionary pattern was associated with pathogenicity, as 63 of the 65 isolates caused wilting of banana and plantain plants under greenhouse conditions, whilst only 32, those isolated from the central region, caused such symptoms in tomato plants. In conclusion, this study shows that banana and plantain crops in Colombia foster genetically diverse strains of R. solanacearum that belong to at least three different genetic groups, which show biogeographic and host range association.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; Ciencias Biológicas y Bioprocesos (CIBIOP)The 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).