Pedagogic Content Knowledge (PCK) in university Biotechnology teaching. The microbial specific growth rate (μ) case

En este trabajo se presenta un análisis de las ideas relacionadas al concepto de velocidad específica de crecimiento microbiano (μ) que presentaron estudiantes universitarios que cursaban la orientación en biotecnología del último año de la carrera de Bioquímica (Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Argentina). El estudio se realizó en base a las respuestas que dieron los estudiantes, de manera anónima,  frente a la solicitud espontanea de que explicaran qué entendían por μ. El análisis se focalizó en la identificación de los factores que podrían relacionarse con las ideas que mostraron los estudiantes, entre las que se el tratamiento previo del concepto, la tendencia a la reducción funcional, el pragmatismo y la posibilidad de que se trate de concepciones alternativas pero en un campo muy específico y aplicado de las ciencias como es la biotecnología. Se plantean estrategias aplicadas para la reconstrucción del concepto de μ considerando estos factores. Las experiencias y conclusiones que surgen de este trabajo pretenden contribuir al desarrollo del conocimiento didáctico del contenido (CDC) en ciencias aplicadas en general, y para la biotecnología en particular.In this work, a study based on the university student’s conception about microbial specific growth rate (μ) is presented. The study was focused on last year students of the Biochemist career (Buenos Aires University, Argentina). It was developed considering the answers given anonymously by the students when they were spontaneously asked about the meaning of μ. The analysis was focused in the identification of factors which could be related with the students´ ideas about μ, such as the previous work with the subject, the tendency to the functional reduction, the pragmatisms and the possibility of alternative conceptions, but related with a specific field of applied sciences, such as biotechnology. Strategies aiming to the reconstruction of the μ concept were proposed considering these factors. The experiences presented in this work will contribute to the development of the Pedagogical Content Knowledge (PCK) in applied sciences, particularly in biotechnology.Fil: Ruberto, Lucas Adolfo Mauro. Universidad de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay; ArgentinaFil: Mac Cormack, Walter P.. Universidad de Buenos Aires; ArgentinaFil: Calabró López, Roberto Ariel. Universidad de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay; ArgentinaFil: Rodriguez Talou, Julian. Universidad de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay; Argentin

Detection of presumed genes encoding beta-lactamases by sequence based screening of metagenomes derived from Antarctic microbial mats

Analysis of environmental samples for bacterial antibiotic resistance genes may have different objectives and analysis strategies. In some cases, the purpose was to study diversity and evolution of genes that could be grouped within a mechanism of antibiotic resistance. Different protocols have been designed for detection and confirmation that a functional gene was found. In this study, we present a sequence-based screening of candidate genes encoding beta-lactamases in 14 metagenomes of Antarctic microbial mats. The samples were obtained from different sites, representing diverse biogeographic regions of maritime and continental Antarctica. A protocol was designed based on generation of Hidden Markov Models from the four beta-lactamase classes by Ambler classification,using sequences from the Comprehensive Antibiotic Resistance Database (CARD). The models were used as queries for metagenome analysis and recovered contigs were subsequently annotated using RAST. According to our analysis, 14 metagenomes analyzed contain A, B and C beta-lactamase genes.Class D genes, however, were identified in 11 metagenomes. The most abundant was class C (46.8%), followed by classes B (35.5%), A (14.2%) and D (3.5%). A considerable number of sequences formed clusters which included, in some cases, contigs from different metagenomes. These assemblies are clearly separated from reference clusters, previously identified using CARD beta-lactamase sequences.While bacterial antibiotic resistance is a major challenge of public health worldwide, our results suggest that environmental diversity of beta-lactamase genes is higher than that currently reported, although this should be complemented with gene function analysis.Fil: Azziz, Gastón. Universidad de la República; UruguayFil: Gimentz, Matìas. Universidad de la República; UruguayFil: Romero, Hèctor. Universidad de la República; UruguayFil: Valdespino Castillo, P.. Lawrence Berkeley National Laboratory; Estados UnidosFil: Falcòn, Luisa I.. Universidad Nacional Autónoma de México; MéxicoFil: Ruberto, Lucas Adolfo Mauro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Nanobiotecnología. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Nanobiotecnología; ArgentinaFil: Mac Cormack, Walter Patricio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Nanobiotecnología. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Nanobiotecnología; ArgentinaFil: Batista, Silvia. Universidad de la República; Urugua

Prospecting biotechnologically-relevant monooxygenases from cold sediment metagenomes: An in silico approach

Source at https://doi.org/10.3390/md15040114.The goal of this work was to identify sequences encoding monooxygenase biocatalysts with novel features by in silico mining an assembled metagenomic dataset of polar and subpolar marine sediments. The targeted enzyme sequences were Baeyer–Villiger and bacterial cytochrome P450 monooxygenases (CYP153). These enzymes have wide-ranging applications, from the synthesis of steroids, antibiotics, mycotoxins and pheromones to the synthesis of monomers for polymerization and anticancer precursors, due to their extraordinary enantio-, regio-, and chemo- selectivity that are valuable features for organic synthesis. Phylogenetic analyses were used to select the most divergent sequences affiliated to these enzyme families among the 264 putative monooxygenases recovered from the ~14 million protein-coding sequences in the assembled metagenome dataset. Three-dimensional structure modeling and docking analysis suggested features useful in biotechnological applications in five metagenomic sequences, such as wide substrate range, novel substrate specificity or regioselectivity. Further analysis revealed structural features associated with psychrophilic enzymes, such as broader substrate accessibility, larger catalytic pockets or low domain interactions, suggesting that they could be applied in biooxidations at room or low temperatures, saving costs inherent to energy consumption. This work allowed the identification of putative enzyme candidates with promising features from metagenomes, providing a suitable starting point for further developments

Una rica colección de bacterias marinas antárticas (Caleta Potter, islas Shetlands del Sur) revela diversos filotipos endémicos y previamente no descritos

La riqueza bacteriana de la Antártida marítima ha sido pobremente descripta hasta la actualidad. En este trabajo se estudió la filogenia de un grupo de colecciones bacterianas planctónicas obtenidas de agua de mar de tres localizaciones cercanas a la base científica argentina antártica Jubany (actualmente Carlini). Sesenta secuencias clonadas del ARN 16S fueron agrupadas filogenéticamente en las clases Alfaproteobacteria  (30/60 clones), Gammaproteobacteria (19/60 clones), Betaproteobacteria (2/60) y Cytophaga?Flavobacteriia?Bacteroides [CFB (3 / 60)]. Por otro lado, seis de las sesenta secuencias (6/60) no pudieron ser clasificadas en ningún grupo conocido. Tanto las Alfaproteobacteria como las Gammaproteobacteria mostraron secuencias no descriptas con anterioridad y eventualmente endémicas. También es remarcable la ausencia de Cyanobacteria en esta biblioteca. En conclusión, estamos publicando aquí una rica colección de secuencias bacterianas de origen marino compuesta por una mayoría de secuencias ampliamente divergentes entre sí y también distantes de aquellas más intimamente relacionadas dentro de las depositadas hasta el presente en los bancos de datos.Fil: Landone Vescovo, Ignacio A.. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Virología; ArgentinaFil: Golemba, Marcelo Darío. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Di Lello, Federico Alejandro. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Culasso, Andrés Carlos Alberto. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Levin, Gustavo. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología Industrial y Biotecnología; ArgentinaFil: Ruberto, Lucas Adolfo Mauro. Ministerio de Relaciones Exteriores, Comercio Interno y Culto. Dirección Nacional del Antártico. Instituto Antártico Argentino; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología Industrial y Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Mac Cormack, Walter P.. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología Industrial y Biotecnología; Argentina. Ministerio de Relaciones Exteriores, Comercio Interno y Culto. Dirección Nacional del Antártico. Instituto Antártico Argentino; ArgentinaFil: López, José L.. Universidad Nacional de la Plata. Facultad de Ciencias Veterinarias. Departamento de Microbiología. Cátedra de Virología; Argentin

Effect of isolation temperature on the characteristics of extracellular proteases produced by Antarctic bacteria

Protease-producing psychrotolerant bacteria were isolated from Antarctic biotopes on casein agar plates using different incubation temperatures. Most of the isolates were non-spore-forming Gram-negative motile rods with catalase activity, 30% were pigmented and none of them were glucose fermenters. All the strains were grown in liquid cultures at 20°C and protease secretion was tested using the azocasein method. Despite their capacity for production of a clear zone of hydrolysis in agar plates, some strains did not produce detectable levels of proteolytic activity in liquid cultures. The lowest apparent optimum temperature for protease activity found in culture supernatants was 40°C. Almost all the strains showed activation energy values about 10-20 kJ-mol?1 lower than that observed for a mesophilic Subtilisin. Most of the proteases showed optimal activity at neutral or alkaline pH values and developed a multiple-band profile on gelatine-SDS-PAGE. It was observed that the lower the strain isolation temperature was, the more stongly cold-adapted–in terms of optimal temperature and activation energy–were the proteases produced by them. This dependence of the characteristics of the proteases on the isolation temperature is an important factor to take into account in the design of screening programmes directed towards the isolation of psychrotolerant bacteria able to produce proteases strongly or weakly adapted to work in the cold. The Antarctic area explored proved to be a promising source of proteolytic bacteria with potential use in industrial processes to be carried out at low or moderate temperatures

Effect of solar radiation and the subsequent dark periods on two newly isolated and characterized Antarctic marine bacteria

Two strains of psychrotolerant Antarctic marine bacteria were isolated and characterized using biochemical and molecular techniques. Sequencing of 16S rRNA gene showed that UVvi strain belongs to the genus Arthrobacter whereas UVps strain is related to the Flexibacter-Cytophaga-Bacteroides (FCB) group. Response of the strains to solar radiation was studied during the summer of 1999 in Potter Cove, near Jubany station (South Shetland Island, Antarctica). The effect of photosynthetically available radiation (PAR, 400-700 nm), ultraviolet-A (UV-A, 320-400 nm) and ultraviolet-B radiation (UV-B, 280-320 nm) on cell viability was studied using mixed cultures in quartz bottles covered with interferential filters and exposed to solar radiation. In all experiments, four treatments were used: dark (with light screened out), PAR (with UV radiation screened out), PAR+UV-A (UV-B screened out) and PAR+UV-A+UV-B. Under the assayed conditions, PAR+UV-A and PAR+UV-A+UV-B radiation showed similar negative effects on the viability of the studied strains. However, at the end of the exposure time, mortality values in PAR+UV-A+UV-B treatments were higher than those observed under PAR+UV-A treatments. In both PAR+UV-A and PAR+UV-A+UV-B treatments we observed high levels of hydrogen peroxide compared with the dark control. The Arthrobacter UVvi strain showed significant recovery in dark conditions after exposure to the PAR+UV-A but not after the PAR+UV-A+UV-B treatment. This strain proved to be more resistant to UV radiation than the FCB group-related UVps strain. The results showed that UV radiation has a deleterious effect on these Antarctic marine bacteria and also revealed that the analysed components of the Antarctic bacterioplankton may have different responses when they are exposed to the same irradiance conditions

The water column as an attenuating factor of the UVR effects on bacteria from a coastal Antarctic marine environment

The effect of UVR on the viability of the culturable bacterial community fraction (CBC), and two of their isolated components (Arthrobacter-UVvi and Bizionia-UVps), was studied in the top few metres of the water column at Potter Cove, King George Island, Antarctica. Quartz flasks containing CBC from surface waters were exposed to solar radiation at depths of 0, 1 and 3 m. Similar experiments using UVps and UVvi isolates were performed. In some experiments interferential filters were used to discriminate photosynthetic active radiation (PAR), UV-A and UV-B. CBC from depths of 0, 10 and 30 m were also exposed to surface solar radiation. The deleterious effect of UVR was observed at the surface and at a depth of 1 m, but not at a depth of 3 m. Studies with interferential filters showed low bacterial viability values at depths of 0 and 1 m under both UVR treatments. However, under low radiation doses the effect attributed to UV-B was higher than that caused by UV-A. The surface CBC was more resistant to UVR compared with CBC from a depth of 30 m. The results showed that CBC inhabiting waters above the pycnocline (located at a depth of 5–10 m) are more efficiently adapted to UVR than are those from below the pycnocline. The impact of UVR on the marine bacterioplankton studied was only detected in the first metre of the stratified water column of Potter Cove, which has high levels of suspended particulate matter. These results support the evidence for a significant UVR-attenuating effect in the water column of this coastal Antarctic water

Changes in salinity and temperature drive marine bacterial communities’ structure at Potter Cove, Antarctica

Coastal areas of the West Antarctic Peninsula (WAP) constitute a rich and biodiverse marine zone. Despite these ecosystems being supported by the microorganism’s activity, the structure of microbial communities is insufficiently studied. As WAP is the area most affected by global warming worldwide, the increased glacier melting caused by the global warming and the consequent increase of the water runoff could be deeply affecting these microbial communities. To advance knowledge about the structure of microbial communities and its response to the environmental factors, a full-year study of marine bacterioplankton was conducted at Potter Cove, Antarctica. Multivariate analysis based on denaturing gradient gel electrophoresis (DGGE) and environmental data revealed a seasonal pattern in the structure of the bacterioplankton community, with spring–summer clustering separately from autumn–winter samples. Salinity, temperature and particulated matter were the main environmental driving forces. Based on the seasonal patterns, five bacterial clone libraries were performed from three sampling sites (E1, inner cove; E2, outer cove; and E3, mouth of a creek). Phylogenetic analysis of libraries generated 301 operational taxonomic units (OTUs), revealing the enormous richness and high diversity of these communities. Proteobacteria (68%), Bacteroidetes (20%) and Actinobacteria (8%) were the most represented phyla. During summer, bacterial community from E1 resembled that observed in E3, whereas during winter it resembled the E2 community. Results evidenced the influence of glacial meltwater input and showed the high variability of the bacterioplankton from inner cove. This study contributes to the better understanding of the structure of the Potter Cove marine ecosystems and could be reflecting the behavior of other similar ecosystems from WAP