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The identification of bacteria plays an essential role in multiple areas of research. Those areas include experimental biology, food and water industries, pathology, microbiology, and evolutionary studies. Although there exist methodologies for identification, a transition to a whole-genome sequence-based taxonomy is already undergoing. Next-Generation Sequencing helps the transition by producing DNA sequence data efficiently. However, the rate of DNA sequence data generation and the high dimensionality of such data need faster computer methodologies. Machine learning, an area of artificial intelligence, has the ability to analyze high dimensional data in a systematic, fast, and efficient way. Therefore, we propose a sequential deep learning model for bacteria identification. The proposed neural network exploits the vast amounts of information generated by Next-Generation Sequencing, in order to extract an identification model for whole-genome bacteria sequences. After validating the identification model, the bidirectional recurrent neural network outperformed other classification approaches.

Abstract Background Providencia rettgeri is a nosocomial pathogen associated with urinary tract infections and related to Healthcare-Associated Infection (HAI). In recent years isolates producing New Delhi Metallo-β-lactamase (NDM) and other β-lactamases have been reported that reduce the efficiency of clinical antimicrobial treatments. In this study, we analyzed antibiotic resistance, the presence of resistance genes and the clonal relationship of two P. rettgeri isolates obtained from male patients admitted to the same hospital in Bogotá – Colombia, 2015. Results Antibiotic susceptibility profile evaluated by the Kirby-Bauer method revealed that both isolates were resistant to third-generation carbapenems and cephalosporins. Whole-genome sequencing (Illumina HiSeq) followed by SPAdes assembling, Prokka annotation in combination with an in-house Python program and resistance gene detection by ResFinder identified the same six β-lactamase genes in both isolates: bla NDM-1 , bla VIM-2 , bla CTX-M-15 , bla OXA-10 , bla CMY-2 and bla TEM-1. Additionally, various resistance genes associated with antibiotic target alteration (arnA, PmrE, PmrF, LpxA, LpxC, gyrB, folP, murA, rpoB, rpsL, tet34) were found and four efflux pumps (RosAB, EmrD, mdtH and cmlA). The additional resistance to gentamicin in one of the two isolates could be explained by a detected SNP in CpxA (Cys191Arg) which is involved in the stress response of the bacterial envelope. Genome BLAST comparison using CGView, the ANI value (99.99%) and the pangenome (using Roary) phylogenetic tree (same clade, small distance) showed high similarity between the isolates. The rMLST analysis indicated that both isolates were typed as rST-61,696, same as the RB151 isolate previously isolated in Bucaramanga, Colombia, 2013, and the FDAARGOS_330 isolate isolated in the USA, 2015. Conclusions We report the coexistence of the carbapenemase genes bla NDM-1, and bla VIM-2, together with the β-lactamase genes bla CTX-M-15 , bla OXA-10 , bla CMY-2 and bla TEM-1, in P. rettgeri isolates from two patients in Colombia. Whole-genome sequence analysis indicated a circulation of P. rettgeri rST-61,696 strains in America that needs to be investigated further.

Societal Impact Statement Colombia is a “megadiverse” country with vast natural resources. A history of recent conflict means that information is only now being collected on the natural capital of regions that were previously unexplored. Better access to data, tools, and expertise is required for evidence‐supported decisions on the conservation of these resources. The development of a bespoke cyberinfrastructure could help fulfill this need by providing access to digital resources in a collaborative cyberenvironment. We outline key priorities and develop a reference framework for building cyberinfrastructure in Colombia. This framework could be applied to other fields and countries to promote knowledge exchange, scientific innovation, and socioeconomic growth.

Background: Gold nanoparticles (AuNPs) can inhibit pivotal pathological changes in experimental asthma, but their effect on steroid-insensitive asthma is unclear. The current study assessed the effectiveness of nebulized AuNPs in a murine model of glucocorticoid (GC)-resistant asthma. Methods: A/J mice were sensitized and subjected to intranasal instillations of ovalbumin (OVA) once a week for nine weeks. Two weeks after starting allergen stimulations, mice were subjected to Budesonide or AuNP nebulization 1 h before stimuli. Analyses were carried out 24 h after the last provocation. Results: We found that mice challenged with OVA had airway hyperreactivity, eosinophil, and neutrophil infiltrates in the lung, concomitantly with peribronchiolar fibrosis, mucus production, and pro-inflammatory cytokine generation compared to sham-challenged mice. These changes were inhibited in mice treated with AuNPs, but not Budesonide. In the GC-resistant asthmatic mice, oxidative stress was established, marked by a reduction in nuclear factor erythroid 2-related factor 2 (NRF2) levels and catalase activity, accompanied by elevated values of thiobarbituric acid reactive substances (TBARS), phosphoinositide 3-kinases δ (PI3Kδ) expression, as well as a reduction in the nuclear expression of histone deacetylase 2 (HDAC2) in the lung tissue, all of which sensitive to AuNPs but not Budesonide treatment. Conclusion: These findings suggest that AuNPs can improve GC-insensitive asthma by preserving HDAC2 and NRF2.

A series of coumarin derivatives and isosteres were synthesized from the reaction of triflic intermediates with phenylboronic acids, terminal alkynes, and organozinc compounds through palladium-catalyzed cross-coupling reactions. The in vitro cytotoxic effect of the compounds was evaluated against two non-small cell lung carcinoma (NSCLC) cell lines (A-549 and H2170) and a normal cell line (NIH-3T3) using cisplatin as a reference drug. Additionally, the effects of the most promising coumarin derivative (9f) in reversing the epithelial-to-mesenchymal transition (EMT) in IL-1β-stimulated A549 cells and in inhibiting the EMT-associated migratory ability in A549 cells were also evaluated. 9f had the greatest cytotoxic effect (CC50 = 7.1 ± 0.8 and 3.3 ± 0.5 μM, respectively against A549 and H2170 cells) and CC50 value of 25.8 µM for NIH-3T3 cells. 9f inhibited the IL-1β-induced EMT in epithelial cells by inhibiting the F-actin reorganization, attenuating changes in the actin cytoskeleton reorganization, and downregulating vimentin in A549 cells stimulated by IL-1β. Treatment of A549 cells with 9f at 7 µM for 24 h significantly reduced the migration of IL-1β-stimulated cells, which is a phenomenon confirmed by qualitative assessment of the wound closure. Taken together, our findings suggest that coumarin derivatives, especially compound 9f, may become a promising candidate for lung cancer therapy, especially in lung cancer promoted by NSCLC cell lines.

Uvaol is a natural pentacyclic triterpene that is widely found in olives and virgin olive oil, exerting various pharmacological properties. However, information remains limited about how it affects fibroblasts and endothelial cells in events associated with wound healing. Here, we report the effect of uvaol in the in vitro and in vivo healing process. We show the positive effects of uvaol on migration of fibroblasts and endothelial cells in the scratch assay. Protein synthesis of fibronectin and laminin (but not collagen type I) was improved in uvaol-treated fibroblasts. In comparison, tube formation by endothelial cells was enhanced after uvaol treatment. Mechanistically, the effects of uvaol on cell migration involved the PKA and p38-MAPK signaling pathway in endothelial cells but not in fibroblasts. Thus, the uvaol-induced migratory response was dependent on the PKA pathway. Finally, topical treatment with uvaol caused wounds to close faster than in the control treatment using experimental cutaneous wounds model in mice. In conclusion, uvaol positively affects the behavior of fibroblasts and endothelial cells, potentially promoting cutaneous healing.

Background: The purpose of this study was to record and analyze the knowledge of medicinal plant use in the community in urban areas of Maceió city, Brazil. Methods: A total of 113 patients from the basic healthcare unit were assessed. Results: Approximately 95% of the interviewed stated that the plants were used for medicinal purposes. The majority of respondents were women (94.7%) who were between 51-60 years of age. Forty-eight plant species belonging to 28 families were cited as useful for medicinal purposes. The main families encountered were Lamiaceae (16.6%), Asteraceae (8.3%), Myrtaceae (6.2%), Fabaceae (6.2%), Annonaceae (4.1%), Laureaceae (4.1%), Rutaceae (4.1%), and Zingiberaceae (4.1%). These plants were used to treat a wide range of disturbances, including gastrointestinal, respiratory, and cardiovascular diseases. The majority of the respondents used decoctions of leaves that were cultivated in house (58.4%) to make their herbal preparations. The respondents revealed that medicinal plant preparations were safe and unaware of that are risks associated with their use. Conclusions: Medicinal plants still play an important role in the medical practices of the urban population from Maceió, Brazil. Our results highlight the importance of these plants for local people and indicate the need for further scientific investigations to validate their use as a complementary therapy for disease control.

We examined the effect of acute and chronic sprint interval training (SIT), with or without prior caffeine intake, on levels of exercise-induced inflammatory plasma cytokines [interleukin (IL)-6, IL-10, tumor necrosis factor (TNF)-α]. Twenty physically-active men ingested either a placebo (n = 10) or caffeine (n = 10) 1 h before each SIT session(13-s × 30-s sprint/15 s of rest) during six training sessions (2 weeks). The early (before, immediately after, and 45 min after the exercise) and late (24 and 48 h after the exercise) cytokine and creatine kinase (CK) responses were analyzed for the first and last training sessions. Plasma IL-6 and IL-10 peaked 45 min after the exercise, and then returned to basal values within 24 h (p < 0.05) in both groups on both occasions (p > 0.05). On both occasions, and for both groups, plasma TNF-α increased from rest to immediately after the exercise and then decreased at 45 min before reaching values at or below basal levels 48 h after the exercise (p < 0.05). Serum CK increased from rest to 24 and 48 h post-exercise in the first training session (p < 0.05), but did not alter in the last training session for the PLA group (p > 0.05). Serum CK was unchanged in both the first and last training sessions for the CAF group (p > 0.05). Two weeks of SIT induced a late decrease in the IL-6/IL-10 ratio (p < 0.05) regardless of caffeine intake, suggesting an improved overall inflammatory status after training. In conclusion, a single session of SIT induces muscle damage that seems to be mitigated by caffeine intake. Two weeks of SIT improves the late SIT-induced muscle damage and inflammatory status, which seems to be independent of caffeine intake.

Spodoptera frugiperda (Lepidoptera: Noctuidae) is a major pest in maize crops in Colombia, and affects several regions in America. A granulovirus isolated from S. frugiperda (SfGV VG008) has potential as an enhancer of insecticidal activity of previously described nucleopolyhedrovirus from the same insect species (SfMNPV). The SfGV VG008 genome was sequenced and analyzed showing circular double stranded DNA of 140,913 bp encoding 146 putative ORFs that include 37 Baculoviridae core genes, 88 shared with betabaculoviruses, two shared only with betabaculoviruses from Noctuide insects, two shared with alphabaculoviruses, three copies of own genes (paralogs) and the other 14 corresponding to unique genes without representation in the other baculovirus species. Particularly, the genome encodes for important virulence factors such as 4 chitinases and 2 enhancins. The sequence analysis revealed the existence of eight homologous regions (hrs) and also suggests processes of gene acquisition by horizontal transfer including the SfGV VG008 ORFs 046/047 (paralogs), 059, 089 and 099. The bioinformatics evidence indicates that the genome donors of mentioned genes could be alpha- and/or betabaculovirus species. The previous reported ability of SfGV VG008 to naturally co-infect the same host with other virus show a possible mechanism to capture genes and thus improve its fitness.

The decoction of the stem barks from Bowdichia virgilioides KUNTH is a folk remedy used to treat inflammatory disorders in Latin American and Brazil. In the present study, the wound healing activity of aqueous extract of the stem bark from B. virgilioides, called AEBv, was evaluated by the rate of healing by wound contraction and period of epithelization at different days post-wound using the wound excisional model. On day 9, the AEBv-treated animals exhibited significative reduction in the wound area when compared with controls. In wound infected with S. aureus, the AEBv significantly improved the wound contraction when compared to the saline-treated mice. The histological analysis showed that AEBv induced a collagen deposition, increase in the fibroblast count and few inflammatory cells than compared to saline-treated group. The expression of collagen type I was increased in the group treated with AEBv as indicated by immunohistochemical staining. In vitro, the AEBv was effective only against S. aureus but not against P. aeruginosa. Together, the results of this study demonstrate, for the first time, the healing and antimicrobiological effects of aqueous extract of the stem bark from B. virgilioides in the therapy of skin wounds.

A number of viruses show a naturally extended tropism for tumor cells whereas other viruses have been genetically modified or adapted to infect tumor cells. Oncolytic viruses have become a promising tool for treating some cancers by inducing cell lysis or immune response to tumor cells. In the present work, rotavirus strains TRF-41 (G5) (porcine), RRV (G3) (simian), UK (G6-P5) (bovine), Ym (G11-P9) (porcine), ECwt (murine), Wa (G1-P8), Wi61 (G9) and M69 (G8) (human), and five wild-type human rotavirus isolates were passaged multiple times in different human tumor cell lines and then combined in five different ways before additional multiple passages in tumor cell lines. Cell death caused by the tumor cell-adapted isolates was characterized using Hoechst, propidium iodide, 7-AAD, Annexin V, TUNEL, and anti-poly-(ADP ribose) polymerase (PARP) and -phospho-histone H2A.X antibodies. Multiple passages of the combined rotaviruses in tumor cell lines led to a successful infection of these cells, suggesting a gain-of-function by the acquisition of greater infectious capacity as compared with that of the parental rotaviruses. The electropherotype profiles suggest that unique tumor cell-adapted isolates were derived from reassortment of parental rotaviruses. Infection produced by such rotavirus isolates induced chromatin modifications compatible with apoptotic cell death.

Las cefotaximasas (CTX-M) son las beta-lactamasas de espectro extendido más ampliamente diseminadas entre especies de la familia Enterobacteriaceae, y son la causa principal de resistencia en aislamientos causantes de infección intrahospitalaria. El objetivo del presente trabajo fue identificar variantes de cefotaximasas del grupo CTX-M-1 mediante el análisis del polimorfismo conformacional de cadena sencilla (SSCP) de frag-mentos de restricción provenientes de los productos de la amplificación por PCR de los genes blaCTX-M. Con el procedimiento PCR-SSCP estandarizado, en este trabajo se analizaron 49 aislamientos de enterobacterias recolectados en 8 hospitales de Bogotá, D.C., adscritos a la Secretaría Distrital de Salud. Se detectaron las variantes CTX-M-12, CTX-M-15, CTX-M-12a, y CTX-M-1 y una nueva variante denominada CTX-M-60. Todas las variantes fueron detectadas tanto en aislamientos intrahospitalarios como de la comunidad, lo que indica posible movilidad de estos genes desde y hacia los centros hospitalarios. Esta publicación constituye el primer reporte en Colombia de la variante CTXM-12a y la nueva variante evolutiva CTX-M-60. Palabras clave: resistencia microbiana; cefotaximasas (CTX-M); polimorfismo conformacional de cadena sencilla (SSCP); beta-lactamasas de espectro extendido (BLEE); infección hospitalaria. Abstract CTX-M cefotaximases are the most widely distributed extended-spectrum beta-lactamases among Enterobacteriaceae and they are an important cause of microbial resistance in nosocomial infection-causing isolates. The object of this work was to identify group 1 CTX-M cefotaximase variants from PCR amplified blaCTX-M genes by single-stranded conformational polymorphism of restriction fragments (RF-SSCP). We analysed 49 Enterobacteria isolates using the RF-SSCP procedure standardised in this work; isolates were collected from eight hospitals attached to the Bogota Health Secretariat (Secretaría Distrital de Salud). CTX-M-12, CTX-M-15, CTX-M-12a and CTX-M-1 variants were detected as well as a new one, designated CTX-M-60. All variants were detected in hospital and community isolates thereby indicating these genes’ possible high mobility from and towards hospital centres. This study represents the first report in Colombia of CTXM-12a and of the new evolutionary variant: CTX-M-60. Key words: drug resistance; cefotaximase (CTX-M), single-strand conformational polymorphism (SSCP); extended-spectrum beta-lactamase (ESBL); hospital infection.

Este artículo es parte de los resultados de una investigación para conocer el proceso de gestión de la integración social de la investigación de nueve instituciones de educación superior co lombianas. En la investigación se analizaron 21 proyectos de investigación de diferentes áreas de conocimiento y tipo de investigaciones (básica, aplicada e I+D+I). Las técnicas e instrumentos utilizados fueron la entrevista semiestrucrurada o enfocada, el grupo focal y análisis documental. Los resultados muestran que la integración es un proceso complejo que implica transferencia y apropiación y que para que exista una gestión de la integración del conocimiento se necesita no solamente una capacidad de gestión sobre los diferentes temas involucrados en la integración (intencionalidad, actores, estructuras organizacionales), sino que adicionalmente existan requerimientos y exigencias muy concretas en las políticas de Estado para el fomento a la investigación.

Título en español: Análisis genómico del resistoma de la cepa de Acinetobacter baumannii ABIBUN 107m multi-resistente y persistente en hospitales colombianos Título en ingles: Genomic analysis of the resistoma of the strain of Acinetobacter baumannii ABIBUN 107m multi-resistant and persistent in Colombian hospitals Título corto: Análisis genómico del resistoma de la cepa de Acinetobacter baumannii Resumen: Acinetobacter baumannii es una bacteria, causante de infecciones asociadas a la atención en salud como neumonía, septicemia, meningitis e infecciones urinarias entre otras. Se caracteriza por su capacidad para desarrollar y acumular rápidamente una gran variedad de mecanismos de resistencia a antibióticos. En esta investigación se realizó el análisis genómico de una cepa de A. baumannii ABIBUN 107m que forma parte de un clon persistente en hospitales colombianos, resistente a los antibióticos carbapenémicos (imipenem y meropenem), antibióticos de elección en el tratamiento infecciones causadas por este microorganismo. El genoma de esta bacteria fue secuenciado utilizando técnicas de alto rendimiento, ensamblado y anotado, obteniéndose un genoma constituido por 3954000 pb con 56 contigs; consta de 4256 genes con un tamaño promedio de 912 pb; 3796 CDS de los cuales por anotación 2884 se asignaron a COG; 57 tRNA y un porcentaje de GC de 38,74%. A. baumannii ABIBUN 107m es resistente a b-lactámicos, aminoglicósidos, quinolonas, tetraciclina, sulfonamida y colistina. En su genoma se localizaron genes asociados con el perfil de resistencia ya que presenta serin b-lactamasas (blaADC-38, blaOXA-64, blaOXA-23, blaampC-like, blaamp(H)-like), metalo b-lactamasa_B; proteínas de unión a penicilina de elevada masa molecular, secuencias de inserción tipo ISAba1; mutaciones en los genes de DNA girasa y topoisomerasa IV subunidad A (gyrA y parC); enzimas modificadoras de aminoglicósidos (aphA-like, aadA-like); cloranfenicol aciltransferasa (cat) y dehidropteroato sintasa (sul-1). Se identificaron genes pertenecientes a cinco familias de sistemas de eflujo (RND, MATE, MSF, ATP, SMR). Abstract: Acinetobacter baumannii is a bacterium causing health care associated infections such as pneumonia, septicemia, meningitis and urinary infections amongst others. It has great capacity to quickly develop and gather a big variety of drug resistance mechanisms. In this research, the genome of strain A. baumannii ABIBUN 107m was analyzed wich forms part of a persistent clon in Colombian hospitals and it’s also resistant to carbapenems (imipenem and meropenem), which are the election antibiotics for treatment of infections caused by this microorganism. The genome was sequenced using high performance technology, assembled and annotated. As a result, we obtained a 3954000 bp genome, with 56 contigs; 4256 genes with average size of 912 bp; 3796 CDS; 2884 were assigned to COG; 57 tRNA and GC percentage of 38,74%. The A. baumannii strain ABIBUN 107m, is resistant to the following antibiotic groups: b-lactams, aminoglycosides, quinolones, tetracycline, sulfonamide and colistin. Genes associated with this resistance profile were found in A. baumannii ABIBUN 107m genome serino b-lactamases (blaADC-38, blaOXA-64, blaOXA-23, blaampC-like, blaamp(H)-like, metallo b-lactamase_B; High Molecular Mass penicillin binding proteins, ISAba1 type insertion sequences, mutations of DNA gyrase and topoisomerase IV subunit A (gyrA and parC); aminoglycoside modifying enzymes (aphA-like, aadA-like); choramphenicol acyltransferase (cat) and dehydropteroate synthase (sul-1). Genes belonging to five different efflux systems were identified (RND, MATE, MSF, ATP, SMR). Key words: Acinetobacter baumannnii MDR, resistome, Colombia Recibido: febrero 26 de 2014 Aprobado: octubre 17 de 2014

Patrones de polimorfismos de nucleótido único (SNPs) prometen explicar la susceptibilidad genética a desarrollar enfermedades multifactoriales como el Síndrome de fatiga crónica (CFS). La selección usando no solo la menor correlación entre SNPs sino también la mayor correlación con la categoría diagnóstica a predecir es posible mediante un enfoque automatizado basado en el concepto informático de entropía. Por lo anterior, se evaluó este enfoque informático en una base de datos de 101 sujetos, 43 pacientes con CFS y 58 controles. Sorprendentemente la exactitud de predicción fue mayor que con el enfoque clásico basado en desequilibrio de ligamiento (72.8 vs. 62.2% p

ENKI-DB, es un sistema de información taxonómica y molecular de especies propias de la biodiversidad colombiana, accesible vía Internet. Mediante ENKI-DB se tiene acceso inmediato a toda la información taxonómica y molecular presente en las bases de datos SPICA®, SIB, EMBL y UNIPROT para especies propias de la biodiversidad colombiana exclusivamente. Hasta la fecha el sistema ha logrado enlazar 10 808 registros de especies propias de la biodiversidad colombiana (presentes en las bases de datos SIB y SPICA®), para las que han encontrado 1 976 751 registros molecula­res, 96 337 provenientes de las bases de datos de información proteica (UniprotKb, Uniref y Uniparc) y 1 880 414 de la base de datos EMBL de DNA. Aunque esta información se encuentra presente también, de manera independiente, en cada una de estas bases de datos, a través de ENKI- DB los datos son accesibles desde una sola interfase y de manera integrada y depurada. El sistema permite además realizar alineamientos locales utilizando la implementación del algoritmo BLAST del NCBI. ENKI- DB ha sido desarrollado en su totalidad en PHP y PERL, haciendo uso de las librerías Bio-PHP, Bio-PERL y utilizando la base de datos MySQL como repositorio central de información. ENKI-DB es accesible vía Internet, de manera completamente gratuita y pública en la siguiente dirección: http://bioinf.ibun.unal.edu.co/enkidb/ Contacto: cenbio_nal@unal.edu.co Palabras clave: ENKI, molecular, taxonomía, biodiversidad colombiana, bioinformática.

De las cuatro especies de plasmodios capaces de infectar con malaria a los seres humanos, Plasmodium falciparum es el que reviste mayor importancia debido a la severidad en la variante de malaria que produce, mortal en la mayoría de los casos. Esta ha sido la razón fundamental por la cual el conocimiento acerca de la genómica y proteómica de esta especie sea mayor al que se tiene de las demás especies de plasmodios que infectan a los seres humanos. Por otra parte, Plasmodium vivax produce un tipo de malaria menos severa que casi nunca es mortal, pero se encuentra muy extendida a nivel mundial, este hecho hace que el conocimiento acerca de la proteómica y genómica de esta especie sea también de gran importancia. Se realizaron búsquedas de secuencias proteícas con actividad antigénica de P. falciparum, en la porción hasta ahora secuenciada del genoma de P. vivax, las cuales no habían sido descritas previamente en este último. Estas búsquedas fueron realizadas en su totalidad mediante técnicas y herramientas bioinformáticas, estableciendo diversos patrones de alineamiento, así como niveles de similitud no menores al 40%. A pesar de un riguroso enmascaramiento tanto de las secuencias protéicas de P. falciparum, como del genoma de P. vivax, en este último fue evidente una alta presencia de regiones repetitivas que no fueron enmascaradas por ninguna de las fuentes de ADN repetitivo presente en la base de datos de REPBASE, lo cual lleva a pensar que dichas regiones pueden ser específicas de este tipo de organismos. Finalmente se encontraron coincidencias entre 76 secuencias proteicas con actividad antigénica de P. falciparum y el genoma hasta ahora secuenciado de P. vivax, que cumplían con los requisitos mínimos para establecer los niveles de coincidencia, entre las cuales se determinó que cuatro constituyen importantes candidatos a una vacuna contra la malaria producida por P. vivax.