Network analysis of the transcriptional pattern of young and old cells of Escherichia coli during lag phase

Background: The aging process of bacteria in stationary phase is halted if cells are subcultured and enter lag phase and it is then followed by cellular division. Network science has been applied to analyse the transcriptional response, during lag phase, of bacterial cells starved previously in stationary phase for 1 day (young cells) and 16 days (old cells). Results: A genome scale network was constructed for E. coli K-12 by connecting genes with operons, transcription and sigma factors, metabolic pathways and cell functional categories. Most of the transcriptional changes were detected immediately upon entering lag phase and were maintained throughout this period. The lag period was longer for older cells and the analysis of the transcriptome revealed different intracellular activity in young and old cells. The number of genes differentially expressed was smaller in old cells (186) than in young cells (467). Relatively, few genes (62) were up- or down-regulated in both cultures. Transcription of genes related to osmotolerance, acid resistance, oxidative stress and adaptation to other stresses was down-regulated in both young and old cells. Regarding carbohydrate metabolism, genes related to the citrate cycle were up-regulated in young cells while old cells up-regulated the Entner Doudoroff and gluconate pathways and down-regulated the pentose phosphate pathway. In both old and young cells, anaerobic respiration and fermentation pathways were down-regulated, but only young cells up-regulated aerobic respiration while there was no evidence of aerobic respiration in old cells.Numerous genes related to DNA maintenance and replication, translation, ribosomal biosynthesis and RNA processing as well as biosynthesis of the cell envelope and flagellum and several components of the chemotaxis signal transduction complex were up-regulated only in young cells. The genes for several transport proteins for iron compounds were up-regulated in both young and old cells. Numerous genes encoding transporters for carbohydrates and organic alcohols and acids were down-regulated in old cells only. Conclusion: Network analysis revealed very different transcriptional activities during the lag period in old and young cells. Rejuvenation seems to take place during exponential growth by replicative dilution of old cellular components

EstuPlan: Methodology for the development of creativity in the resolution of scientific and social problems

[EN] Creative thinking is necessary to generate novel ideas and solve problems. "EstuPlan" is a methodology in which knowledge and creativity converge for the resolution of scientific problems with social projection. It is a training programme that integrates teachers, laboratory technicians and PhD students, master and undergraduate students which form working groups for the development of projects. Projects have a broad and essential scope and projection in terms of environmental problems, sustainable use of natural resources, food, health, biotechnology or biomedicine. The results show the success of this significant learning methodology using tools to develop creativity in responding to scientific and social demand for problem-solving to transfer academic knowledge to different professional environments. Bioplastics, Second Life of Coffee, LimBio, Algae oils, Ecomers, Caring for the life of your crop and Hate to Deforestate are currently being developed.Astudillo Calderón, S.; De Díez De La Torre, L.; García Companys, M.; Ortega Pérez, N.; Rodríguez Martínez, V.; Alzahrani, S.; Alonso Valenzuela, R.... (2019). EstuPlan: Methodology for the development of creativity in the resolution of scientific and social problems. En HEAD'19. 5th International Conference on Higher Education Advances. Editorial Universitat Politècnica de València. 711-717. https://doi.org/10.4995/HEAD19.2019.9205OCS71171

Aplicación de nuevos agentes antimicrobianos para controlar la seguridad de productos vegetales frescos precortados (IV Gama)

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Ciencia y Tecnologia de los Alimentos e Ingenieria Química. Fecha de lectura 07-11-200

Comparison of Probabilistic and Deterministic Predictions of Time to Growth of Listeria monocytogenes as Affected by pH and Temperature in Food

8 pages, 2 tables, 4 figures.-- Online Ahead of Print: October 8, 2010.-- This is a copy of an article published in the Foodborne Pathogens and Disease © 2011 [copyright Mary Ann Liebert, Inc.]; Foodborne Pathogens and Disease is available online at: http://www.liebertonline.com.Stochastic models are useful for estimating the risk of foodborne illness and they can be integrated, besides other sources of variability, into microbial risk assessment. A stochastic approach to evaluate growth of two strains of Listeria monocytogenes influenced by different factors affecting microbial growth (pH and storage temperature) was performed. An individual-based approach of growth through optical density measurements was used. From results obtained, histograms of the lag phase were generated and distributions were fitted. Histograms presented increased variation when the factors applied were suboptimal for L. monocytogenes and they were combined. The extreme value distribution was ranked as the best one in most cases, whereas normal was the poorest fitting distribution. To evaluate the influence of pH and storage temperature on L. monocytogenes CECT 5672 in real food, commercial samples of courgette and carrot soup were inoculated with this pathogen. It was able to grow in both soups at storage temperatures from 4°C to 20°C. Using the distributions adjusted, predictions of time to growth (102 cfu/g) of L. monocytogenes were established by Monte Carlo simulation and they were compared with deterministic predictions and observations in foods.Dr. Marina Muñoz thanks Fundación CAJAMURCIA for awarding her a fellowship. This project was funded by Ministerio de Educación y Ciencia Español (ref. AGL 2006-13320-C03-02=ALI)Peer reviewe

Modularity quantification in sub-networks extracted from the <i>Salmonella</i> genome scale network containing those genes differentially expressed during and after the heat treatment and comparison with random extracted sub-networks with the same number of genes.

1<p>Modularity coefficient from 0 to 1 (maximum modularity).</p>2<p>Mean value and standard deviation of the modularity coefficient of 10 random networks.</p>*<p>Significant: Smaller than the mean value minus 3 times the standard deviation of random networks.</p

Fold change of transcript levels of genes during heat stress and immediately and 30 minutes after temperature was set back at 25°C that exhibited hysteresis and encoded for heat shock proteins (A), for DNA repair (B) for products involved in protein stabilization (C) or were encoded in plasmids (D).

<p>Down-regulated genes throughout the experiment were associated with non stress specific response such as pathogenesis (E) and motility (F). Genes represented in each plot showed a similar tendency; they are listed by the side of each plot but not differentially represented.</p

Duration of the lag phase and maximum specific growth rate at 43°C and pH 4.5 of <i>S.</i> Typhimurium previously exposed to heat and acid shock.

*<p>mean±standard deviation of 3 independent replicated experiments.</p

Network representation of genes up- and down-regulated during and after the heat shock.

<p>Modularity of networks of down-regulated genes was significantly lower than that of up-regulated networks. The induction of genes belonging to a metabolic pathway or cellular function was more synchronized than their down-regulation because of the hysteretic transcriptional response or persistence of the induction of the majority of genes induced by the heat shock once the temperature is set back to 25°C. Different colours represent different modules in each network.</p

Number of genes up- (green) and down- (red) regulated in <i>S</i>. Typhimurium under acid and heat stressing conditions and immediately and 30 min after removing the stressing conditions.

<p>Few genes were affected by acid stress (A) while transcription of a large number of genes was altered under heat stress (B). Majority of up-regulated genes under heat stress remained up-regulated 30 minutes after stress condition ceased. Black numbers and solid lines show up- and down- regulated genes maintained throughout the experiment.</p