Computational Biology in Costa Rica: The Role of a Small Country in the Global Context of Bioinformatics

Introduction: The successful development of high throughput methods for DNA sequencing, transcriptomics, proteomics, and other –omics, has contributed to the emergence of novel possibilities for the examination of complex biological systems through computational analysis. These fields have witnessed unprecedented advances in high income countries. Nevertheless, the role of other nations needs to be examined in order to delineate their contribution within the global context of bioinformatics. Previous articles have focused on the expansion of Computational Biology in Brazil and Mexico [1],[2], two of the largest Latin American countries, and which have shown political commitment to foster their scientific development. Costa Rica is a small Central American country with a population of 4 million, with its territory 164 and 38 times smaller than Brazil and Mexico, respectively. Thus, it is interesting to visualize the possibilities and challenges of this low-income country in the context of the global bioinformatics endeavor.UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias de la Salud::Instituto Clodomiro Picado (ICP

The outer membranes of Brucella spp. are resistant to bactericidal cationic peptides

The actions of polymyxin B, rabbit polymorphonuclear lysosome extracts, 14 polycationic peptides (including defensin NP-2, cecropin P1, lactoferricin B, and active peptides from cationic protein 18 and bactenecin), EDTA, and Tris on Brucella spp. were studied, with other gram-negative bacteria as controls. Brucella spp. were comparatively resistant to all of the agents listed above and bound less polymyxin B, and their outer membranes (OMs) were neither morphologically altered nor permeabilized to lysozyme by polymyxin B concentrations, although both effects were observed for controls. EDTA and peptides increased or accelerated the partition of the hydrophobic probe N-phenyl-naphthylamine into Escherichia coli and Haemophilus influenzae OMs but had no effect on Brucella OMs. Since Brucella and H. influenzae OMs are permeable to hydrophobic compounds (G. Martínez de Tejada and I. Moriyón, J. Bacteriol. 175:5273-5275, 1993), the results show that such unusual permeability is not necessarily related to resistance to polycations. Although rough (R) B. abortus and B. ovis were more resistant than the controls were, there were qualitative and quantitative differences with smooth (S) brucellae; this may explain known host range and virulence differences. Brucella S-lipopolysaccharides (LPSs) had reduced affinities for polycations, and insertion of Brucella and Salmonella montevideo S-LPSs into the OM of a Brucella R-LPS mutant increased and decreased, respectively, its resistance to cationic peptides. The results show that the core lipid A of Brucella LPS plays a major role in polycation resistance and that O-chain density also contributes significantly. It is proposed that the features described above contribute to Brucella resistance to the oxygen-independent systems of phagocytes

Gemini-GRACES high-quality spectra of Kepler evolved stars with transiting planets: I. Detailed characterization of multi-planet systems Kepler-278 and Kepler-391

Aims. Kepler-278 and Kepler-391 are two of the three evolved stars known to date on the red giant branch (RGB) to host multiple short-period transiting planets. Moreover, the planets orbiting Kepler-278 and Kepler-391 are among the smallest discovered around RGB stars. Here we present a detailed stellar and planetary characterization of these remarkable systems. Methods. Based on high-quality spectra from Gemini-GRACES for Kepler-278 and Kepler-391, we obtained refined stellar parameters and precise chemical abundances for 25 elements. Nine of these elements and the carbon isotopic ratios, 12C∕ 13C, had not previously been measured. Also, combining our new stellar parameters with a photodynamical analysis of the Kepler light curves, we determined accurate planetary properties of both systems. Results. Our revised stellar parameters agree reasonably well with most of the previous results, although we find that Kepler-278 is ~15% less massive than previously reported. The abundances of C, N, O, Na, Mg, Al, Si, S, Ca, Sc, Ti, V, Cr, Mn, Co, Ni, Cu, Zn, Sr, Y, Zr, Ba, and Ce, in both stars, are consistent with those of nearby evolved thin disk stars. Kepler-391 presents a relatively high abundance of lithium (A(Li)NLTE = 1.29 ± 0.09 dex), which is likely a remnant from the main-sequence phase. The precise spectroscopic parameters of Kepler-278 and Kepler-391, along with their high 12C∕ 13C ratios, show that both stars are just starting their ascent on the RGB. The planets Kepler-278b, Kepler-278c, and Kepler-391c are warm sub-Neptunes, whilst Kepler-391b is a hot sub-Neptune that falls in the hot super-Earth desert and, therefore, it might be undergoing photoevaporation of its outer envelope. The high-precision obtained in the transit times allowed us not only to confirm Kepler-278c's TTV signal, but also to find evidence of a previously undetected TTV signal for the inner planet Kepler-278b. From the presence of gravitational interaction between these bodies we constrain, for the first time, the mass of Kepler-278b (Mp = 56 -13+37 M⊕ ) and Kepler-278c (Mp = 35 -21+9.9 M⊕ ). The mass limits, coupled with our precise determinations of the planetary radii, suggest that their bulk compositions are consistent with a significant amount of water content and the presence of H2 gaseous envelopes. Finally, our photodynamical analysis also shows that the orbits of both planets around Kepler-278 are highly eccentric (e ~ 0.7) and, surprisingly, coplanar. Further observations (e.g., precise radial velocities) of this system are needed to confirm the eccentricity values presented here.Fil: Jofré, Edgardo. Universidad Nacional de Córdoba. Observatorio Astronómico de Córdoba. Departamento de Astrofísica Estelar; Argentina. Universidad Nacional Autónoma de México; México. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Almenara, J.M.. Universidad de Ginebra; SuizaFil: Petrucci, Romina Paola. Universidad Nacional de Córdoba. Observatorio Astronómico de Córdoba. Departamento de Astrofísica Estelar; Argentina. Universidad Nacional Autónoma de México; México. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Diaz, Rodrigo Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Astronomía y Física del Espacio. - Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Astronomía y Física del Espacio; ArgentinaFil: Gómez Maqueo Chew, Y.. Universidad Nacional Autónoma de México; MéxicoFil: Martioli, E.. Laboratorio Nacional de Astrofísica; BrasilFil: Ramírez, I.. Tacoma Community College; Estados UnidosFil: García, Luciano Héctor. Universidad Nacional de Córdoba. Observatorio Astronómico de Córdoba. Departamento de Astrofísica Estelar; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Saffe, Carlos. Universidad Nacional de San Juan. Facultad de Ciencias Exactas, Físicas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Juan. Instituto de Ciencias Astronómicas, de la Tierra y del Espacio. Universidad Nacional de San Juan. Instituto de Ciencias Astronómicas, de la Tierra y del Espacio; ArgentinaFil: Canul, E. F.. Universidad Nacional Autónoma de México; MéxicoFil: Buccino, Andrea Paola. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Astronomía y Física del Espacio. - Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Astronomía y Física del Espacio; ArgentinaFil: Gómez, Marcos Javier. Universidad Nacional de Córdoba. Observatorio Astronómico de Córdoba. Departamento de Astrofísica Estelar; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Moreno Hilario, E.. Universidad Nacional Autónoma de México; Méxic

Plataforma gamificada que permite la resolución de desafios en legunaje C en el ámbito universitario

La gamificación consiste en utilizar las dinámicas, mecánicas y componentes propios de los juegos en espacios no lúdicos, con el objetivo de motivar a los usuarios para resolver una determinada tarea. En este trabajo se plantea la gamificación en el ámbito universitario, para motivar a los alumnos a realizar ejercicios vinculados con la resolución de problemas en el Lenguaje C en el marco de la materia de Elementos de Programación, que se ubica curricularmente en el primer año de las carreras de Ingeniería que ofrece la Universidad Nacional de La Matanza. La plataforma gamificada presenta los ejercicios de una forma distinta por medio de desafíos y permite la corrección automática de los mismos, tanto desde el punto de vista de la codificación como a través casos de prueba lógica, planificados para corroborar que la resolución cumple con lo requerido en la consigna. Lo que agrega la motivación y jugabilidad es justamente la gamificación por medio de elementos propios de los juegos, en este artículo se presentan los avances del proyecto junto con los nuevos elementos incorporados a la plataforma.Eje: Tecnología Informática Aplicada en Educación.Red de Universidades con Carreras en Informátic

Plataforma gamificada que permite la resolución de desafios en legunaje C en el ámbito universitario

La gamificación consiste en utilizar las dinámicas, mecánicas y componentes propios de los juegos en espacios no lúdicos, con el objetivo de motivar a los usuarios para resolver una determinada tarea. En este trabajo se plantea la gamificación en el ámbito universitario, para motivar a los alumnos a realizar ejercicios vinculados con la resolución de problemas en el Lenguaje C en el marco de la materia de Elementos de Programación, que se ubica curricularmente en el primer año de las carreras de Ingeniería que ofrece la Universidad Nacional de La Matanza. La plataforma gamificada presenta los ejercicios de una forma distinta por medio de desafíos y permite la corrección automática de los mismos, tanto desde el punto de vista de la codificación como a través casos de prueba lógica, planificados para corroborar que la resolución cumple con lo requerido en la consigna. Lo que agrega la motivación y jugabilidad es justamente la gamificación por medio de elementos propios de los juegos, en este artículo se presentan los avances del proyecto junto con los nuevos elementos incorporados a la plataforma.Eje: Tecnología Informática Aplicada en Educación.Red de Universidades con Carreras en Informátic

Plataforma gamificada que permite la resolución de desafios en legunaje C en el ámbito universitario

La gamificación consiste en utilizar las dinámicas, mecánicas y componentes propios de los juegos en espacios no lúdicos, con el objetivo de motivar a los usuarios para resolver una determinada tarea. En este trabajo se plantea la gamificación en el ámbito universitario, para motivar a los alumnos a realizar ejercicios vinculados con la resolución de problemas en el Lenguaje C en el marco de la materia de Elementos de Programación, que se ubica curricularmente en el primer año de las carreras de Ingeniería que ofrece la Universidad Nacional de La Matanza. La plataforma gamificada presenta los ejercicios de una forma distinta por medio de desafíos y permite la corrección automática de los mismos, tanto desde el punto de vista de la codificación como a través casos de prueba lógica, planificados para corroborar que la resolución cumple con lo requerido en la consigna. Lo que agrega la motivación y jugabilidad es justamente la gamificación por medio de elementos propios de los juegos, en este artículo se presentan los avances del proyecto junto con los nuevos elementos incorporados a la plataforma.Eje: Tecnología Informática Aplicada en Educación.Red de Universidades con Carreras en Informátic

Brucella-Salmonella lipopolysaccharide chimeras are less permeable to hydrophobic probes and more sensitive to cationic peptides and EDTA than are their native Brucella sp. counterparts

A rough (R) Brucella abortus 45/20 mutant was more sensitive to the bactericidal activity of polymyxin B and lactoferricin B than was its smooth (S) counterpart but considerably more resistant than Salmonella montevideo. The outer membrane (OM) and isolated lipopolysaccharide (LPS) of S. montevideo showed a higher affinity for these cationic peptides than did the corresponding B. abortus OM and LPS. We took advantage of the moderate sensitivity of R B. abortus to cationic peptides to construct live R B. abortus-S-LPS chimeras to test the activities of polymyxin B, lactoferricin B, and EDTA. Homogeneous and abundant peripheral distribution of the heterologous S-LPS was observed on the surface of the chimeras, and this coating had no effect on the viability or morphology of the cells. When the heterologous LPS corresponded to the less sensitive bacterium S B. abortus S19, the chimeras were more resistant to cationic peptides; in contrast, when the S-LPS was from the more sensitive bacterium S. montevideo, the chimeras were more susceptible to the action of peptides and EDTA. A direct correlation between the amount of heterologous S-LPS on the surface of chimeric Brucella cells and peptide sensitivity was observed. Whereas the damage produced by polymyxin B in S. montevideo and B. abortus-S. montevideo S-LPS chimeras was manifested mainly as OM blebbing and inner membrane rolling, lactoferricin B caused inner membrane detachment, vacuolization, and the formation of internal electron-dense granules in these cells. Native S and R B. abortus strains were permeable to the hydrophobic probe N-phenyl-1-naphthylamine (NPN). In contrast, only reduced amounts of NPN partitioned into the OMs of the S. montevideo and B. abortus-S. montevideo S-LPS chimeras. Following peptide exposure, accelerated NPN uptake similar to that observed for S. montevideo was detected for the B. abortus-S. montevideo LPS chimeras. The partition of NPN into native or EDTA-, polymyxin B-, or lactoferricin B-treated LPS micelles of S. montevideo or B. abortus mimicked the effects observed with intact cells, and this was confirmed by using micelle hybrids of B. abortus and S. montevideo LPSs. The results showed that LPS is the main cause of B. abortus' resistance to bactericidal cationic peptides, the OM-disturbing action of divalent cationic chelants, and OM permeability to hydrophobic substances. It is proposed that these three features are related to the ability of Brucella bacteria to multiply within phagocytes

What have we learned from brucellosis in the mouse model?

Brucellosis is a zoonosis caused by Brucella species. Brucellosis research in natural hosts is often precluded by practical, economical and ethical reasons and mice are widely used. However, mice are not natural Brucella hosts and the course of murine brucellosis depends on bacterial strain virulence, dose and inoculation route as well as breed, genetic background, age, sex and physiological statu of mice. Therefore, meaningful experiments require a definition of these variables. Brucella spleen replication profiles are highly reproducible and course in four phases: i), onset or spleen colonization (first 48 h); ii), acute phase, from the third day to the time when bacteria reach maximal numbers; iii), chronic steady phase, where bacterial numbers plateaus; and iv), chronic declining phase, during which brucellae are eliminated. This pattern displays clear physiopathological signs and is sensitive to small virulence variations, making possible to assess attenuation when fully virulent bacteria are used as controls. Similarly, immunity studies using mice with known defects are possible. Mutations affecting INF-gamma, TLR9, Myd88, T gamma delta and TNF-beta favor Brucella replication; whereas IL-1 beta, IL-18, TLR4, TLR5, TLR2, NOD1, NOD2, GM-CSF, IL/17r, Rip2, TRIF, NK or Nramp1 deficiencies have no noticeable effects. Splenomegaly development is also useful: it correlates with IFN-gamma and IL-12 levels and with Brucella strain virulence. The genetic background is also important: Brucella-resistant mice (C57BL) yield lower splenic bacterial replication and less splenomegaly than susceptible breeds. When inoculum is increased, a saturating dose above which bacterial numbers per organ do not augment, is reached. Unlike many gram-negative bacteria, lethal doses are large (>= 10(8) bacteria/mouse) and normally higher than the saturating dose. Persistence is a useful virulence/attenuation index and is used in vaccine (Residual Virulence) quality control. Vaccine candidates are also often tested in mice by determining splenic Brucella numbers after challenging with appropriate virulent brucellae doses at precise post-vaccination times. Since most live or killed Brucella vaccines provide some protection in mice, controls immunized with reference vaccines (S19 or Rev1) are critical. Finally, mice have been successfully used to evaluate brucellosis therapies. It is concluded that, when used properly, the mouse is a valuable brucellosis model

Brucellosis and one health: inherited and future challenges

One Health is the collaborative efforts of multiple disciplines to attain optimal health for people, animals and the environment, a concept that historically owes much to the study of brucellosis, including recent political and ethical considerations. Brucellosis One Health actors include Public Health and Veterinary Services, microbiologists, medical and veterinary practitioners and breeders. Brucellosis awareness, and the correct use of diagnostic, epidemiological and prophylactic tools is essential. In brucellosis, One Health implementation faces inherited and new challenges, some aggravated by global warming and the intensification of breeding to meet growing food demands. In endemic scenarios, disease awareness, stakeholder sensitization/engagement and the need to build breeder trust are unresolved issues, all made difficult by the protean characteristics of this zoonosis. Extended infrastructural weaknesses, often accentuated by geography and climate, are critically important. Capacity-building faces misconceptions derived from an uncritical adoption of control/eradication strategies applied in countries with suitable means, and requires additional reference laboratories in endemic areas. Challenges for One Health implementation include the lack of research in species other than cattle and small ruminants, the need for a safer small ruminant vaccine, the need to fill in the infrastructure gap, the need for realistic capacity-building, the creation of reference laboratories in critical areas, and the stepwise implementation of measures not directly transposed from the so-called developed countries

Gamificación en el ámbito universitario : Análisis e implementación de elementos de juegos

La gamificación consiste en agregar elementos de juegos a espacios no lúdicos. En este caso se aplica al ámbito universitario. Se toma como punto de partida un proyecto anterior del equipo de trabajo donde se desarrolló e implementó una plataforma de gamificación para la enseñanza de programación en la cual se proponen una serie de desafíos al alumno, que consisten en resolver distintos problemas codificando una función y asignado de forma automática puntaje según los errores cometidos ya sean sintácticos o lógicos. Esa asignación de puntos es un ejemplo de lo que se conoce como componentes en la gamificación. Con dichos puntos se generó un ranking general y un ranking por cursos lo que hace que el alumno se vea motivado por la competencia (mecánica de juego) y la autosatisfacción de lograr un puesto mejor (dinámica de juego). Este proyecto se basa en analizar y determinar nuevos elementos de juegos que pueden ser incorporados más allá de los puntos y rankings ya incorporados previamente. El agregado de nuevos componentes permitirá generar nuevas mecánicas y dinámicas que harán más atractiva a la plataforma fomentando la utilización de la misma por parte de los estudiantes.Eje: Tecnología Informática Aplicada en Educación.Red de Universidades con Carreras en Informática (RedUNCI