Mitigar la propagación de la COVID - 19 : un desafío y una oportunidad

(Eng) The Colombian government declared the quarantine for all the population since 25th March, 2020 as a measure to mitigate the expansion of COVID-19 in the country. Nevertheless, this restrictive measure showed early some opposite consequences to its purpose. As observed in other countries, the restriction measure caused a mass purchase of products, formation of crowds in grocery, department stores and local markets. The fear of shortage also caused exhaustion of products, long journeys and accumulation of large numbers of people in stores, bank offices and ATMs

Microbial cultivation in rocking single-use bioreactors

The application of single-use bioreactors (SUB) for microbial cultivation, especially of reactor designs beyond the traditional stirred tank, is usually regarded as crucial. Especially the usually low gas mass transfer coefficients are insufficient, however this is not true for 2-dimensionally rocking motion bioreactors like the CELL-tainer®. Volumetric gas mass transfer coefficients (kLa-values) of 600 h-1 are achieved (fig. 1), which allow bacterial fed-batch cultivations up to a cell density of 50 gL-1 at growth rates of 0.3 h-1 w/o any oxygen blending (Junne et al, Chem Eng Technol 2013, 85, p. 57-66). One major asset in this respect are the low maximum shear forces in comparison to stirred tank reactors. This feature might be beneficial when shear sensitive microbes are cultivated, like marine phototrophic and heterotrophic microalgae and filamentous organisms. Please click Additional Files below to see the full abstract

Robustifying Experimental Tracer Design for13C-Metabolic Flux Analysis

13C metabolic flux analysis (MFA) has become an indispensable tool to measure metabolic reaction rates (fluxes) in living organisms, having an increasingly diverse range of applications. Here, the choice of the13C labeled tracer composition makes the difference between an information-rich experiment and an experiment with only limited insights. To improve the chances for an informative labeling experiment, optimal experimental design approaches have been devised for13C-MFA, all relying on some a priori knowledge about the actual fluxes. If such prior knowledge is unavailable, e.g., for research organisms and producer strains, existing methods are left with a chicken-and-egg problem. In this work, we present a general computational method, termed robustified experimental design (R-ED), to guide the decision making about suitable tracer choices when prior knowledge about the fluxes is lacking. Instead of focusing on one mixture, optimal for specific flux values, we pursue a sampling based approach and introduce a new design criterion, which characterizes the extent to which mixtures are informative in view of all possible flux values. The R-ED workflow enables the exploration of suitable tracer mixtures and provides full flexibility to trade off information and cost metrics. The potential of the R-ED workflow is showcased by applying the approach to the industrially relevant antibiotic producer Streptomyces clavuligerus, where we suggest informative, yet economic labeling strategies

Streptomyces clavuligerus shows a strong association between TCA cycle intermediate accumulation and clavulanic acid biosynthesis

Clavulanic acid (CA) is produced by Streptomyces clavuligerus (S. clavuligerus) as a secondary metabolite. Knowledge about the carbon flux distribution along the various routes that supply CA precursors would certainly provide insights about metabolic performance. In order to evaluate metabolic patterns and the possible accumulation of tricarboxylic acid (TCA) cycle intermediates during CA biosynthesis, batch and subsequent continuous cultures with steadily declining feed rates were performed with glycerol as the main substrate. The data were used to in silico explore the metabolic capabilities and the accumulation of metabolic intermediates in S. clavuligerus. While clavulanic acid accumulated at glycerol excess, it steadily decreased at declining dilution rates; CA synthesis stopped when glycerol became the limiting substrate. A strong association of succinate, oxaloacetate, malate, and acetate accumulation with CA production in S. clavuligerus was observed, and flux balance analysis (FBA) was used to describe the carbon flux distribution in the network. This combined experimental and numerical approach also identified bottlenecks during the synthesis of CA in a batch and subsequent continuous cultivation and demonstrated the importance of this type of methodologies for a more advanced understanding of metabolism; this potentially derives valuable insights for future successful metabolic engineering studies in S. clavuligerus.BMBF, 01DN16018, Schnellere Prozessentwicklung für Bioprodukt

Metabolic adaptation of two in silico mutants of Mycobacterium tuberculosis during infection

ABSTRACT: Background: Up to date, Mycobacterium tuberculosis (Mtb) remains as the worst intracellular killer pathogen. To establish infection, inside the granuloma, Mtb reprograms its metabolism to support both growth and survival, keeping a balance between catabolism, anabolism and energy supply. Mtb knockouts with the faculty of being essential on a wide range of nutritional conditions are deemed as target candidates for tuberculosis (TB) treatment. Constraint-based genome-scale modeling is considered as a promising tool for evaluating genetic and nutritional perturbations on Mtb metabolic reprogramming. Nonetheless, few in silico assessments of the effect of nutritional conditions on Mtb’s vulnerability and metabolic adaptation have been carried out. Results: A genome-scale model (GEM) of Mtb, modified from the H37Rv iOSDD890, was used to explore the metabolic reprogramming of two Mtb knockout mutants (pfkA- and icl-mutants), lacking key enzymes of central carbon metabolism, while exposed to changing nutritional conditions (oxygen, and carbon and nitrogen sources). A combination of shadow pricing, sensitivity analysis, and flux distributions patterns allowed us to identify metabolic behaviors that are in agreement with phenotypes reported in the literature. During hypoxia, at high glucose consumption, the Mtb pfkA-mutant showed a detrimental growth effect derived from the accumulation of toxic sugar phosphate intermediates (glucose-6-phosphate and fructose-6-phosphate) along with an increment of carbon fluxes towards the reductive direction of the tricarboxylic acid cycle (TCA). Furthermore, metabolic reprogramming of the icl-mutant (icl1&icl2) showed the importance of the methylmalonyl pathway for the detoxification of propionyl-CoA, during growth at high fatty acid consumption rates and aerobic conditions. At elevated levels of fatty acid uptake and hypoxia, we found a drop in TCA cycle intermediate accumulation that might create redox imbalance. Finally, findings regarding Mtb-mutant metabolic adaptation associated with asparagine consumption and acetate, succinate and alanine production, were in agreement with literature reports. Conclusions: This study demonstrates the potential application of genome-scale modeling, flux balance analysis (FBA), phenotypic phase plane (PhPP) analysis and shadow pricing to generate valuable insights about Mtb metabolic reprogramming in the context of human granulomas

Bibliometric Analysis of Global Research on Clavulanic Acid

Clavulanic acid (CA), a potent inhibitor of the β-lactam, ase enzyme, is frequently co-formulated with a broad spectrum of antibiotics to treat infections caused by β-lactamase-producing pathogens. In order to evaluate the impact and the progress of CA studies in the last four decades, a bibliometric analysis of the global scientific production of CA was carried out. A total of 39,758 records in the field of CA were indexed in the Scopus database for a 43-year period of study (1975⁻2017). The results indicated that CA studies have grown, showing three phases (1975⁻1999, 2000⁻2003 and 2004⁻2017) based on records of publications; the results showed a sigmoidal profile. Medicine was the main subject area for CA studies, whereas biochemistry, genetics and molecular biology were areas of research for CA production by Streptomyces clavuligerus (S. clavuligerus). Nevertheless, chemical engineering (as a subject area) had the highest increase in the percentage of publications related to CA production by S. clavuligerus. The United States, France, the United Kingdom, Spain and Brazil were the leading countries in the scientific production of studies on both CA and CA related to S. clavuligerus. This analysis allowed the identification of the area of knowledge with the highest impact on CA studies, the top researchers and their geographic distribution, and also helped to highlight the existence of antibiotic-resistant bacteria as an emergent area in CA research

Clavulanic Acid Production by Streptomyces clavuligerus: Insights from Systems Biology, Strain Engineering, and Downstream Processing

Clavulanic acid (CA) is an irreversible β-lactamase enzyme inhibitor with a weak antibacterial activity produced by Streptomyces clavuligerus (S. clavuligerus). CA is typically co-formulated with broad-spectrum β‑lactam antibiotics such as amoxicillin, conferring them high potential to treat diseases caused by bacteria that possess β‑lactam resistance. The clinical importance of CA and the complexity of the production process motivate improvements from an interdisciplinary standpoint by integrating metabolic engineering strategies and knowledge on metabolic and regulatory events through systems biology and multi-omics approaches. In the large-scale bioprocessing, optimization of culture conditions, bioreactor design, agitation regime, as well as advances in CA separation and purification are required to improve the cost structure associated to CA production. This review presents the recent insights in CA production by S. clavuligerus, emphasizing on systems biology approaches, strain engineering, and downstream processing

Conceptos básicos de análisis de fluxes metabólicos.

El metabolismo representa el nivel biológico que más se relaciona con los fenotipos de la célula y, las alteraciones o reprogramaciones de éste pueden, entre otras, (i) afectar la producción de metabolitos primarios o secundarios en microorganismos de interés biotecnológico, (ii) favorecer o no la inhibición del crecimiento en organismos patógenos y (iii) desarrollar desórdenes metabólicos como la obesidad o la diabetes. Es por ello, que el estudio del metabolismo, el rediseño, y el redireccionamiento de fluxes metabólicos se ha convertido en un área importante de investigación (también conocida como Ingeniería Metabólica), ya que ha permitido el desarrollo y diseño de procesos biológicos mejorados, la identificación de blancos terapéuticos, el diseño de estrategias terapéuticas para curar desordenes metabólicos y la identificación de biomarcadores en cáncer, entre otros. Actualmente, se han desarrollado metodologías computacionales que permiten estudiar el metabolismo celular a diferentes condiciones medioambientales, dirigiendo la experimentación con las predicciones del modelo. El propósito de esta revisión es resaltar la importancia del análisis de fluxes metabólicos como una metodología general para estudiar la reprogramación metabólica en distintos organismos de interés biotecnológico, médico, y terapéutico. Este trabajo condensa las bases teóricas y los conceptos claves para entender el análisis de fluxes metabólicos, lo cual será un insumo fundamental para aquellos que se están adentrando al mundo de la biología de sistemas o áreas afines

Conceptos básicos de análisis de fluxes metabólicos

Metabolism represents the biological level that is most related to the phenotypes of the cell and, alterations or reprogramming of this can (i) affect the production of primary or secondary metabolites in microorganisms of biotechnological interest, (ii) favor or not the inhibition of growth in pathogenic organisms and (iii) developing metabolic disorders such as obesity or diabetes, among others. The study of metabolism, redesign, and redirection of metabolic fluxes has become an important area of research (also known as Metabolic Engineering), as it has allowed the development and design of improved biological processes, the identification of therapeutic targets, the design of therapeutic strategies to cure metabolic disorders and the identification of biomarkers in cancer, among others. Currently, the development of computational methodologies is allowing to study the cell metabolism under different environmental conditions and directing experiments with the model's predictions. The purpose of this review is to highlight the importance of metabolic flux analysis as a general methodology to study metabolic reprogramming in different organisms of biotechnological, medical, and therapeutic interest. This work condenses the theoretical bases and key concepts to understand the analysis of metabolic fluxes, which will be a fundamental input for those who are entering to the world of systems biology or related areas.El metabolismo representa el nivel biológico que más se relaciona con los fenotipos de la célula y, las alteraciones o reprogramaciones de éste pueden, entre otras, (i) afectar la producción de metabolitos primarios o secundarios en microorganismos de interés biotecnológico, (ii) favorecer o no la inhibición del crecimiento en organismos patógenos y (iii) desarrollar desórdenes metabólicos como la obesidad o la diabetes. Es por ello, que el estudio del metabolismo, el rediseño, y el redireccionamiento de fluxes metabólicos se ha convertido en un área importante de investigación (también conocida como Ingeniería Metabólica), ya que ha permitido el desarrollo y diseño de procesos biológicos mejorados, la identificación de blancos terapéuticos, el diseño de estrategias terapéuticas para curar desordenes metabólicos y la identificación de biomarcadores en cáncer, entre otros. Actualmente, se han desarrollado metodologías computacionales que permiten estudiar el metabolismo celular a diferentes condiciones medioambientales, dirigiendo la experimentación con las predicciones del modelo. El propósito de esta revisión es resaltar la importancia del análisis de fluxes metabólicos como una metodología general para estudiar la reprogramación metabólica en distintos organismos de interés biotecnológico, médico, y terapéutico. Este trabajo condensa las bases teóricas y los conceptos claves para entender el análisis de fluxes metabólicos, lo cual será un insumo fundamental para aquellos que se están adentrando al mundo de la biología de sistemas o áreas afines

Investigaciones en reutilización de antivirales actualmente disponibles en Colombia como alternativas de tratamiento para el COVID-19.

La enfermedad del coronavirus 2019 (COVID-19) fue declarada pandemia en marzo de 2020 por la Organización Mundial de la Salud. Esta enfermedad respiratoria es causada por el nuevo síndrome respiratorio agudo severo coronavirus 2 (SARS-CoV-2) y los esfuerzos actuales se centran en encontrar alternativas farmacéuticas y vacunas para ambos, prevenir y tratar a los pacientes infectados en todo el mundo. Después de los períodos de cuarentena, el tratamiento de la enfermedad aún se limita al manejo de la sintomatología y la remisión a las unidades de cuidados críticos de los casos más graves. América acumula el mayor número de casos y bajas y el aumento de la presión sobre la economía llevó a relajar las medidas de mitigación. Se han realizado varios ensayos clínicos con antivirales como alternativas disponibles a corto plazo para hacer frente a la creciente tasa de contagios, mientras las vacunas experimentales se desarrollan y prueban adecuadamente. La literatura científica hace referencia a un conjunto de medicamentos aprobados por la FDA como compuestos reutilizados con acción potencial sobre el mecanismo viral del SARS-CoV-2. En Colombia algunas de esas sustancias se comercializan actualmente como antivirales y antiparasitarios de venta libre, mientras que otros medicamentos también en el panorama no están disponibles, pero son potencialmente accesibles en el corto plazo para el tratamiento del COVID-19 en Colombia, hasta que una campaña de vacunación masiva se puede desplegar en el país