Multiwavelength studies of MHD waves in the solar chromosphere: An overview of recent results

The chromosphere is a thin layer of the solar atmosphere that bridges the relatively cool photosphere and the intensely heated transition region and corona. Compressible and incompressible waves propagating through the chromosphere can supply significant amounts of energy to the interface region and corona. In recent years an abundance of high-resolution observations from state-of-the-art facilities have provided new and exciting ways of disentangling the characteristics of oscillatory phenomena propagating through the dynamic chromosphere. Coupled with rapid advancements in magnetohydrodynamic wave theory, we are now in an ideal position to thoroughly investigate the role waves play in supplying energy to sustain chromospheric and coronal heating. Here, we review the recent progress made in characterising, categorising and interpreting oscillations manifesting in the solar chromosphere, with an impetus placed on their intrinsic energetics.Comment: 48 pages, 25 figures, accepted into Space Science Review

The European Solar Telescope

The European Solar Telescope (EST) is a project aimed at studying the magnetic connectivity of the solar atmosphere, from the deep photosphere to the upper chromosphere. Its design combines the knowledge and expertise gathered by the European solar physics community during the construction and operation of state-of-the-art solar telescopes operating in visible and near-infrared wavelengths: the Swedish 1m Solar Telescope, the German Vacuum Tower Telescope and GREGOR, the French Télescope Héliographique pour l'Étude du Magnétisme et des Instabilités Solaires, and the Dutch Open Telescope. With its 4.2 m primary mirror and an open configuration, EST will become the most powerful European ground-based facility to study the Sun in the coming decades in the visible and near-infrared bands. EST uses the most innovative technological advances: the first adaptive secondary mirror ever used in a solar telescope, a complex multi-conjugate adaptive optics with deformable mirrors that form part of the optical design in a natural way, a polarimetrically compensated telescope design that eliminates the complex temporal variation and wavelength dependence of the telescope Mueller matrix, and an instrument suite containing several (etalon-based) tunable imaging spectropolarimeters and several integral field unit spectropolarimeters. This publication summarises some fundamental science questions that can be addressed with the telescope, together with a complete description of its major subsystems

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

The European Solar Telescope

The European Solar Telescope (EST) is a project aimed at studying the magnetic connectivity of the solar atmosphere, from the deep photosphere to the upper chromosphere. Its design combines the knowledge and expertise gathered by the European solar physics community during the construction and operation of state-of-the-art solar telescopes operating in visible and near-infrared wavelengths: the Swedish 1m Solar Telescope, the German Vacuum Tower Telescope and GREGOR, the French Télescope Héliographique pour l’Étude du Magnétisme et des Instabilités Solaires, and the Dutch Open Telescope. With its 4.2 m primary mirror and an open configuration, EST will become the most powerful European ground-based facility to study the Sun in the coming decades in the visible and near-infrared bands. EST uses the most innovative technological advances: the first adaptive secondary mirror ever used in a solar telescope, a complex multi-conjugate adaptive optics with deformable mirrors that form part of the optical design in a natural way, a polarimetrically compensated telescope design that eliminates the complex temporal variation and wavelength dependence of the telescope Mueller matrix, and an instrument suite containing several (etalon-based) tunable imaging spectropolarimeters and several integral field unit spectropolarimeters. This publication summarises some fundamental science questions that can be addressed with the telescope, together with a complete description of its major subsystems

Bacterial contamination of automotive fuels in a tropical region: the case of Costa Rica

Microbial contamination of fuel has been the cause of several problems in transportation and storage of these products. Due to the lack of previous studies related to these problems in Costa Rica, bacterial quality was evaluated biannually in automotive fuels stored in the four oil distribution facilities of the Costa Rican Petroleum Refinery (RECOPE). In 12 oil storage tanks, for a total of 96 samples, mesophilic, heterotrophic aerobic/facultative counts (ASTM D6974-04) and identification of bacteria presented in regular gas, premium gas and diesel from the bottom and superior part of the tanks were done; in the samples containing an aqueous phase, sulfate reducing bacteria (SRB) were also quantified by the most probable number technique (MPN), according to the ASTM D4412-84 standard. The higher contamination was shown at the bottom of the tanks (populations up to 10(4) UFC/l), especially if there was accumulated water, in which case populations reached 10(8) UFC/l. The most contaminated fuel was diesel (counts up to 10(4) UFC/l), whereas the less contaminated was premium gas. The less contaminated fuels were from the facilities of La Garita and Barranca, whereas the most contaminated were from Ochomogo. Nevertheless, the quantified populations did not cause significant alteration in quality physicochemical parameters in the samples analyzed. A total of 149 bacterial strains were isolated, 136 (91.3%) Gram positive and 13 (8.7%) Gram negative. The most frequent genera were Staphylococcus (24.0%), Micrococcus (21.9%), Bacillus (18.8%) and Kocuria (11.5%) among Gram positive bacteria and Pseudomonas (7.3%) among Gram negative bacteria. The majority of these genera have been found as fuel contaminants or even as degraders of this kind of products; nevertheless, some species for which their appearance or growth in hydrocarbons have not been described were found with low frequencies. SRB were present in counts up to 10(5) MPN/l in 42.9% of water containing samples (including all from diesel tanks), indicating biocorrosion processes risk in fuel transport and storage systems. From the findings in this study it is recommended to give a frequent maintenance to fuel containers, based on continuous drainage and removal of accumulated water, antimicrobial agent addition and microbial quality monitoring in country’s fuels. Rev. Biol. Trop. 57 (3): 489-504. Epub 2009 September 30.<br>Se evaluó semestralmente durante dos años la calidad bacteriana de los combustibles almacenados en los cuatro planteles de la Refinadora Costarricense de Petróleo (Costa Rica). Para un total de 96 muestras se realizaron recuentos (norma ASTM D6974-04) e identificación de las bacterias presentes en gasolina regular, gasolina súper y diesel en los niveles superior e inferior de los tanques contenedores; en las muestras con fase acuosa se cuantificaron las bacterias reductoras de sulfato (SRB, norma ASTM D4412-84). La mayor contaminación se observó en el fondo de los tanques, sobretodo si se presentó una capa de agua almacenada. El diesel fue el combustible más contaminado, sin embargo, no se observó alteración importante en los parámetros fisicoquímicos de las muestras evaluadas. Se aislaron 149 cepas, 136 (91.3%) Gram positivas y 13 (8.7%) Gram negativas; los géneros más frecuentes fueron Staphylococcus (24.0%), Micrococcus (21.9%), Bacillus (18.8%), Kocuria (11.5%) y Pseudomonas (7.3%). Con bajas frecuencias se encontraron algunas especies para las que no se ha descrito su aparición o crecimiento en hidrocarburos. Las SRB se presentaron con recuentos de hasta 105 MPN/l en un 42.9% de las muestras con agua residual, principalmente en diesel, lo cual es indicativo de alerta por biocorrosión. A partir de los resultados se recomienda dar un mantenimiento frecuente a los contenedores, la adición de compuestos antimicrobianos y el monitoreo de la calidad microbiana de los combustibles del país

Bacterial contamination of automotive fuels in a tropical region: the case of Costa Rica

Microbial contamination of fuel has been the cause of several problems in transportation and storage of these products. Due to the lack of previous studies related to these problems in Costa Rica, bacterial quality was evaluated biannually in automotive fuels stored in the four oil distribution facilities of the Costa Rican Petroleum Refinery (RECOPE). In 12 oil storage tanks, for a total of 96 samples, mesophilic, heterotrophic aerobic/facultative counts (ASTM D6974-04) and identification of bacteria presented in regular gas, premium gas and diesel from the bottom and superior part of the tanks were done; in the samples containing an aqueous phase, sulfate reducing bacteria (SRB) were also quantified by the most probable number technique (MPN), according to the ASTM D4412-84 standard. The higher contamination was shown at the bottom of the tanks (populations up to 104 UFC/l), especially if there was accumulated water, in which case populations reached 108 UFC/l. The most contaminated fuel was diesel (counts up to 104 UFC/l), whereas the less contaminated was premium gas. The less contaminated fuels were from the facilities of La Garita and Barranca, whereas the most contaminated were from Ochomogo. Nevertheless, the quantified populations did not cause significant alteration in quality physicochemical parameters in the samples analyzed. A total of 149 bacterial strains were isolated, 136 (91.3%) Gram positive and 13 (8.7%) Gram negative. The most frequent genera were Staphylococcus (24.0%), Micrococcus (21.9%), Bacillus (18.8%) and Kocuria (11.5%) among Gram positive bacteria and Pseudomonas (7.3%) among Gram negative bacteria. The majority of these genera have been found as fuel contaminants or even as degraders of this kind of products; nevertheless, some species for which their appearance or growth in hydrocarbons have not been described were found with low frequencies. SRB were present in counts up to 105 MPN/l in 42.9% of water containing samples (including all from diesel tanks), indicating biocorrosion processes risk in fuel transport and storage systems. From the findings in this study it is recommended to give a frequent maintenance to fuel containers, based on continuous drainage and removal of accumulated water, antimicrobial agent addition and microbial quality monitoring in country's fuels

Bioadsorção de niquel por Acinetobacter baumannii e Pseudomonas aeruginosa isoladas de águas residuais industriais

Nickel biosorption ability was evaluated in two bacterial strains: Acinetobacter baumannii UCR-2971 and Pseudomonas aeruginosa UCR-2957, resulting in greatest adsorption at pH 4.5 and a residence time of 100 minutes. Biosorption isotherms showed that the process follows the Langmuir model. The maximum adsorption rates (Nmax) were 8.8 and 5.7 mg·g-1 for A. baumannii and P. aeruginosa, respectively; however, affinity constants suggest that P. aeruginosa (K=1.28) has higher affinity for nickel than A. baumannii (K=0.68). It is suggested that both strains could be used for wastewater treatment, as long as the concentration of Ni2+ is within the range of mg·L-1.Foi avaliada a capacidade de adsorção do Ni2+ por duas bactérias, Acinetobacter baumannii e Pseudomonas aeruginosa, em pH 4.5 com tempo de contato de 100 minutos. Isotermas de adsorção foram calculadas com as duas linhagens. Observou-se que, para ambas, o processo de adsorção está de acordo com o modelo fisicoquímico de Langmuir. A captação máxima do Ni2+ (Nmax) foi 5.7 e 8.8 mg Ni2+ g -1 para P. aeruginosa e A. baumannii, respectivamente. Não obstante, P. aeruginosa apresenta uma constante de afinidade (K=1.28) maior que A. baumannii (K=0.68). Estes resultados indicam que ambas as linhagens são adequadas para o tratamento de águas contaminadas, desde que a concentração de níquel seja da ordem de mg·L-1.UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias de la Salud::Centro de Investigación en Enfermedades Tropicales (CIET)UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro en Investigación en Contaminación Ambiental (CICA)UCR::Vicerrectoría de Docencia::Salud::Facultad de Microbiologí

Bacteroides fragilis group in non-diarrheic human feces and its antimicrobial susceptibility

Bacteroides es el género de bacterias anaerobias predominante en el colon humano, y sus diez especies son la causa de la mayoría de las infecciones anaerobias. Ya que casi todas las infecciones que causan son endógenas, el conocimiento de su resistencia es importante por la posible diseminación de ésta. Se analizaron 80 muestras de heces humanas que fueron sembradas en agar BBE (Bacteroides Bile Esculin) y KVLB (Kanamycin, Vancomycin, Laked Blood) y se incubaron en anaerobiosis 48 horas a 35 ºC. La identificación y la determinación de la sensibilidad se realizaron con los sistemas Rapid ID-32 A y ATB ANA (BioMerieux), respectivamente. En 64 de las 80 muestras (80%) se en contró al menos una especie del grupo B. fragilis, siendo B. uniformis y B. fragilis las más frecuentes (24,6% y 16,9%), y B. stercoris y B. eg gerthii las menos frecuentes (0,7% y 2,1%). Las cepas mostraron resistencia a diversas penicilinas (de 93,1% a 40,2%), en ocasiones inclu so en presencia de ácido clavulánico, así como a las cefalosporinas (de 31,0% a 52,1%), la clindamicina (32,2%) y el imipenem (10,3%). Los antibióticos más efectivos fueron la piperacilina y la ticarcilina asociados con inhibidores de betalactamasas, el cloranfenicol y el metronida zol (más del 90% de sensibilidad). Aunque ningún B. fragilis fue resistente a la clindamicina ni al metronidazol, un tercio de las cepas resis tentes al imipenem eran de esta especie. La más resistente fue B. distasonis y la más sensible B. vulgatus. Ninguno de los fármacos evalua dos fue efectivo contra todas las especies del grupo; en la mayoría de las especies hubo cepas con resistencia al imipenem, al metronidazol o a la clindamicina, lo que sugiere la existencia de mecanismos eficientes de transmisión de resistencia entre bacterias endógenas.Bacteroides is a predominant anaerobic bacteria of the human colon. Since the ten species of the Bacteroides fragilis group are responsible for most anaerobic endogenous infections, the antimicrobial resistance of these bacteria is of great concern due to the role they can play in the dissemination of resistance. Eighty non-diarrheic human feces samples were analyzed. Each sample was inoculated in BBE (Bacteroides Bile Esculin) and KVLB (Kanamycin, Vancomycin, Laked Blood) agar plates and were incubated in anaerobic conditions for 48 h at 35ºC. For identification and antimicrobial sensitivity, miniaturized systems for anaerobic bacteria (Rapid ID-32A and ATB ANA, Biomerieux) were used. Sixty-four (80%) of the samples were positive for at least one Bacteroides fragilis species; B. uniformis and B. fragilis were the most frequent species (24.6% and 16.9%); B. stercoris and B. eggerthii were the least frequent (0.7 and 2.1%). The strains showed resistance to different penicillins (40.2-93.1%), some even in the presence of beta-lactamase inhibitors; to cephalosporins (31.0-52.1%) and to frequently used antibiotics against anaerobes, such as clindamycin (32.2%) and imipenem (10.3%). The most effective antimicrobials against Bacteroides fragilis were piperacillin and ticarcillin combined with beta-lactamase inhibitors, as well as chloramphenicol and metronidazole (>90% sus ceptibility). None of the B. fragilis group were resistant to clindamycin or metronidazole, but one-third of the imipenem-resistant strains be longed to this species. The most resistant species was B. distasonis, while B. vulgatus was the most susceptible. None of the tested antimi crobials were effective against all ten species; the majority of the species had some isolates that were resistant to imipenem, metronidazole or clindamycin. This resistance pattern suggests the presence of efficient transmission mechanisms among these endogenous bacteria.UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias de la Salud::Centro de Investigación en Enfermedades Tropicales (CIET)UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro en Investigación en Contaminación Ambiental (CICA)UCR::Vicerrectoría de Docencia::Salud::Facultad de Microbiologí

Flora Bacteriana de la Cavidad Oral del Mono Tití (Saimiri Oerstedii) Y su Perfil de Sensibilidad a Antibióticos

Se estudió la flora bacteriana y su patrón de sensibilidad antimicrobiana en la cavidad oral de 33 monos Saimiri oerstedii: 31 silvestres y 2 en cautiverio. Con torunda estéril se rasparon los dientes y la cavidad bucal de cada mono y se resuspendió en 2 mL de solución salina estéril (0.85%); se prepararon tubos de transporte para cultivos aerobios y anaerobios y una vez en el laboratorio, se inocularon placas de agar sangre que se incubaron en aerobiosis y anaerobiosis. Los aislamientos se iden tificaron con sistemas miniaturizados API® (20NE, Staph y 20A); las determinaciones de la sensibilidad a los antibióticos se realizaron con galerías ATB® (G5, Staph y ANA). Se aislaron 137 cepas bacterianas: 106 aerobias (77.4%) y 31 anaerobias (22.6%). El predominio fue de bacilos Gram negativos aerobios (100 cepas), siendo Enterobacter el género más frecuente (42%), seguido de Burkholderia y Aeromonas (27% c/u); los anaerobios más comunes fueron Clostridium (36%) y Fuso bacterium (12%). Estos resultados revelan semejanzas y diferencias con respecto a la flora oral humana y la de otros monos costarricenses; la alta frecuencia de algunos géneros sugiere que son parte de la flora oral de monos y no contaminación secundaria de bacterias del suelo. El 90% de los bacilos Gram negativos aerobios fue resistente a cefalotina y el 89% a cefoxi tina; altas tasas de resistencia se presentaron también ante otras drogas; solamente ceftriaxone y pefloxacina fueron efectivos contra todas las cepas analizadas; sólo dos cepas fueron sensibles a todos los antibióticos evaluados. El mayor porcentaje de resistencia en anaerobios ocurrió ante el metronidazole (26 a 35%) seguido por cefotetán (26%) y clindamicina (23%); el 39% de los aislamientos fue sensible a todos los antibióticos evaluados. La resistencia múltiple fue menor en los anaerobios (26%) que en los aerobios (77%). Este estudio contribuye al conocimiento y a la preservación del mono tití, especie ame nazada, y muestra que pocas barreras son capaces de contener los genes de resistencia y sus hospederos bacterianos, aun en animales silvestres.The bacterial microflora present in the oral cavity of 33 squirrel monkeys (Saimiri oerstedii, 31 wild and 2 captive) and its an timicrobial sensibility was studied. A sterile swab was used to scratch the teeth and oral cavity of every monkey; each sample was resuspended in 2 mL sterile saline solution (0.85%). Transport tubes for aerobic and anaerobic cultures inoculated with these samples were sent to the laboratory. Each sample was inoculated in blood agar plates that were incubated in aerobic and anaerobic conditions. Isolates obtained were identified with API™ galleries (20NE, Staph and 20A) and the sensibility determinations were done using ATB galleries (-G5, -Staph and -ANA). A total of 137 strains were isolated: 106 aerobes (77.4%) and 31 anaerobes (22.6%). Gram negative bacilli were predominant, with Enterobacter the most frequent genus (42%), followed by Burkholderia and Aeromonas (27% each). The most frequent anaerobes were Clostridium (36%) and Fusobacterium (12%). These results show similarities and differences with the bacteria of the oral cavity of humans and of other Costa Rican monkeys. The high frequency of some genera suggests that they are part of the oral flora of the monkeys and not contaminants from the soil. Ninety percent of the Gram negative aerobe bacilli were resistant to cephalotin and 89% to cefoxitine. High resistance rates were obtained with other agents; only two strains were sensitive to every antibiotic tested. In anaerobes the higher antibiotic resistance was observed with metronidazole (26–35%), cefotetan (20%) and clindamicyn (23%), 39% of the strains were sensitive to every antibiotic tested; multiple resistance was lower in the anaerobes (26%) than in the aerobes (77%). This study contributes to the knowledge and preservation of the squirrel monkey, a threatened species, and demonstrates that there are few barriers to the spread of resistant genes in bacteria, even in wild animals.UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro en Investigación en Contaminación Ambiental (CICA)UCR::Vicerrectoría de Docencia::Salud::Facultad de MicrobiologíaUCR::Sedes Regionales::Sede de OccidenteUCR::Vicerrectoría de Docencia::Ciencias Básicas::Facultad de Ciencias::Escuela de Biologí