Quorum sensing influences growth and photosynthetic membrane production in high-cell-density cultivations of Rhodospirillum rubrum

BACKGROUND: The facultative anoxygenic photosynthetic bacterium Rhodospirillum rubrum exhibits versatile metabolic activity allowing the adaptation to rapidly changing growth conditions in its natural habitat, the microaerobic and anoxic zones of stagnant waters. The microaerobic growth mode is of special interest as it allows the high-level expression of photosynthetic membranes when grown on succinate and fructose in the dark, which could significantly simplify the industrial production of compounds associated with PM formation. However, recently we showed that PM synthesis is no longer inducible when R. rubrum cultures are grown to high cell densities under aerobic conditions. In addition a reduction of the growth rate and the continued accumulation of precursor molecules for bacteriochlorophyll synthesis were observed under high cell densities conditions. RESULTS: In the present work, we demonstrate that the cell density-dependent effects are reversible if the culture supernatant is replaced by fresh medium. We identified six N-acylhomoserine lactones and show that four of them are produced in varying amounts according to the growth phase and the applied growth conditions. Further, we demonstrate that N-acylhomoserine lactones and tetrapyrrole compounds released into the growth medium affect the growth rate and PM expression in high cell density cultures. CONCLUSIONS: In summary, we provide evidence that R. rubrum possesses a Lux-type quorum sensing system which influences the biosynthesis of PM and the growth rate and is thus likely to be involved in the phenotypes of high cell density cultures and the rapid adaptation to changing environmental conditions

Quality of Web Mashups: A Systematic Mapping Study

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-319-04244-2_8Web mashups are a new generation of applications based on the composition of ready-to-use, heterogeneous components. They are gaining momentum thanks to their lightweight composition approach, which represents a new opportunity for companies to leverage on past investments in SOA, Web services, and public APIs. Although several studies are emerging in order to address mashup development, no systematic mapping studies have been reported on how quality issues are being addressed. This paper reports a systematic mapping study on which and how the quality of Web mashups has been addressed and how the product quality-aware approaches have been defined and validated. The aim of this study is to provide a background in which to appropriately develop future research activities. A total of 38 research papers have been included from an initial set of 187 papers. Our results provided some findings regarding how the most relevant product quality characteristics have been addressed in different artifacts and stages of the development process. They have also been useful to detect some research gaps, such as the need of more controlled experiments and more quality-aware mashup development proposals for other characteristics which being important for the Web domain have been neglected such as Usability and ReliabilityThis work is funded by the MULTIPLE project (TIN2009-13838), the Senescyt program (scholarships 2011), and the Erasmus Mundus Programme of the European Commission under the Transatlantic Partnership for Excellence in Engineering - TEE Project.Cedillo Orellana, IP.; Fernández Martínez, A.; Insfrán Pelozo, CE.; Abrahao Gonzales, SM. (2013). Quality of Web Mashups: A Systematic Mapping Study. En Current Trends in Web Engineering. Springer. 66-78. https://doi.org/10.1007/978-3-319-04244-2_8S6678Alkhalifa, E.: The Future of Enterprise Mashups. Business Insights. E-Strategies for Resource Management Systems (2009)Beemer, B., Gregg, D.: Mashups: A Literature Review and Classification Framework. Future Internet 1, 59–87 (2009)Cappiello, C., Daniel, F., Matera, M.: A Quality Model for Mashup Components. In: Gaedke, M., Grossniklaus, M., Díaz, O. (eds.) ICWE 2009. LNCS, vol. 5648, pp. 236–250. Springer, Heidelberg (2009)Cappiello, C., Daniel, F., Matera, M., Pautasso, C.: Information Quality in Mashups. IEEE Internet Computing 14(4), 32–40 (2010)Cappiello, C., Matera, M., Picozzi, M., Daniel, F., Fernandez, A.: Quality-Aware Mashup Composition: Issues, Techniques and Tools. In: 8th International Conference on the Quality of Information and Communications Technology (QUATIC 2012), pp. 10–19 (2012)Fenton, N.E., Pfleeger, S.L.: Software Metrics: A Rigorous and Practical Approach, 2nd edn. International Thompson 1996, pp. I–XII, 1–638 (1996) ISBN 978-1-85032-275-7Fernandez, A., Insfran, E., Abrahão, S.: Usability evaluation methods for the web: A systematic mapping study. Information and Software Technology 53(8), 789–817 (2011)Garousi, V., Mesbah, A., Betin-Can, A., Mirshokraie, S.: A systematic mapping study of web application testing. Information and Software Technology 55(8), 1374–1396 (2013)Grammel, L., Storey, M.-A.: A survey of mashup development environments. In: Chignell, M., Cordy, J., Ng, J., Yesha, Y. (eds.) The Smart Internet. LNCS, vol. 6400, pp. 137–151. Springer, Heidelberg (2010)Hoyer, V., Fischer, M.: Market Overview of Enterprise Mashup Tools. In: Bouguettaya, A., Krueger, I., Margaria, T. (eds.) ICSOC 2008. LNCS, vol. 5364, pp. 708–721. Springer, Heidelberg (2008)ISO/IEC: ISO/IEC 25010 Systems and software engineering. Systems and software Quality Requirements and Evaluation (SQuaRE). System and software quality models (2011)Kitchenham, B., Charters, S.: Guidelines for performing Systematic Literature Reviews in Software Engineering. Version 2.3, ESBE Technical Report, Keele University, UK (2007)Mendes, E.: A systematic review on the Web engineering research. In: International Symposium on Empirical Software Engineering (ISESE 2005), pp. 498–507 (2005)OrangeLabs: State of the Art in Mashup tools, SocEDA project, pp. 1–59 (2011)Petersen, K., Feldt, R., Mujtaba, S., Mattsson, M.: Systematic mapping studies in software engineering. In: 12th International Conference on Evaluation and Assessment in Software Engineering (EASE), pp. 68–77 (2008)Raza, M., Hussain, F.K., Chang, E.: A methodology for quality-based mashup of data sources. In: 10th International Conference on Information Integration and Web-based Applications & Services (iiWAS 2008), pp. 528–533 (2008)Saeed, A.: A Quality-based Framework for Leveraging the Process of Mashup Component Selection (2009), https://gupea.ub.gu.se/handle/2077/21953Sharma, A., Hellmann, T.D., Maurer, F.: Testing of Web Services - A Systematic Mapping. In: 8th World Congress on Services (SERVICES 2012), pp. 346–352 (2012

Use of approximations of Hamilton-Jacobi-Bellman inequality for solving periodic optimization problems

We show that necessary and sufficient conditions of optimality in periodic optimization problems can be stated in terms of a solution of the corresponding HJB inequality, the latter being equivalent to a max-min type variational problem considered on the space of continuously differentiable functions. We approximate the latter with a maximin problem on a finite dimensional subspace of the space of continuously differentiable functions and show that a solution of this problem (existing under natural controllability conditions) can be used for construction of near optimal controls. We illustrate the construction with a numerical example.Comment: 29 pages, 2 figure

Profiling of external metabolites during production of hantavirus nucleocapsid protein with recombinant Saccharomyces cerevisiae

Recombinant strains of Saccharomyces cerevisiae, producing hantavirus Puumala nucleocapsid protein for diagnostics and as a candidate vaccine were analyzed for uptake and excretion of intermediary metabolites during process optimization studies of fed-batch bioreactor cultures. Concentrations of glucose, maltose, galactose, pyruvate, acetaldehyde, ethanol, acetate, succinate and formaldehyde (used as a selection agent) were measured in the culture medium in order to find a metabolite pattern, indicative for the physiological state of the producer culture. When the inducer galactose was employed as a growth substrate, the metabolite profile of recombinant yeast cells was different from those of the non-recombinant original strain which excreted considerable amounts of metabolites with this substrate. In contrast, galactose-induced heterologous gene expression was indicated by the absence of excreted intermediary metabolites, except succinate. A model strain expressing a GFP fusion of hantavirus nucleocapsid protein differed in the excretion of metabolites from strains without GFP. In addition, the influence of alkali ions, employed for pH control is also demonstrated

Live-cell imaging of alkyne-tagged small biomolecules by stimulated Raman scattering

Sensitive and specific visualization of small biomolecules in living systems is highly challenging. We report stimulated Raman-scattering imaging of alkyne tags as a general strategy for studying a broad spectrum of small biomolecules in live cells and animals. We demonstrate this technique by tracking alkyne-bearing drugs in mouse tissues and visualizing de novo synthesis of DNA, RNA, proteins, phospholipids and triglycerides through metabolic incorporation of alkyne-tagged small precursors

The Photosynthetic Apparatus and Its Regulation in the Aerobic Gammaproteobacterium Congregibacter litoralis gen. nov., sp. nov

BACKGROUND: There is accumulating evidence that in some marine environments aerobic bacteriochlorophyll a-producing bacteria represent a significant part of the microbial population. The interaction of photosynthesis and carbon metabolism in these interesting bacteria is still largely unknown and requires further investigation in order to estimate their contribution to the marine carbon cycle. METHODOLOGY/PRINCIPAL FINDINGS: Here, we analyzed the structure, composition and regulation of the photosynthetic apparatus in the obligately aerobic marine gammaproteobacterium KT71(T). Photoheterotrophically grown cells were characterized by a poorly developed lamellar intracytoplasmic membrane system, a type 1 light-harvesting antenna complex and a photosynthetic reaction center associated with a tetraheme cytochrome c. The only photosynthetic pigments produced were bacteriochlorophyll a and spirilloxanthin. Under semiaerobic conditions KT71(T) cells expressing a photosynthetic apparatus showed a light-dependent increase of growth yield in the range of 1.3-2.5 fold. The expression level of the photosynthetic apparatus depended largely on the utilized substrate, the intermediary carbon metabolism and oxygen tension. In addition, pigment synthesis was strongly influenced by light, with blue light exerting the most significant effect, implicating that proteins containing a BLUF domain may be involved in regulation of the photosynthetic apparatus. Several phenotypic traits in KT71(T) could be identified that correlated with the assumed redox state of growing cells and thus could be used to monitor the cellular redox state under various incubation conditions. CONCLUSIONS/SIGNIFICANCE: In a hypothetical model that explains the regulation of the photosynthetic apparatus in strain KT71(T) we propose that the expression of photosynthesis genes depends on the cellular redox state and is maximal under conditions that allow a balanced membrane redox state. So far, bacteria capable of an obligately aerobic, photosynthetic metabolism constitute a unique phenotype within the class Gammaproteobacteria, so that it is justified to propose a new genus and species, Congregibacter litoralis gen. nov, sp. nov., represented by the type strain KT71(T) ( = DSM 17192(T) = NBRC 104960(T))

Evaluating Process Quality Based on Change Request Data – An Empirical Study of the Eclipse Project

Abstract. The information routinely collected in change request management systems contains valuable information for monitoring of the process quality. However this data is currently utilized in a very limited way. This paper presents an empirical study of the process quality in the product portfolio of the Eclipse project. It is based on a systematic approach for the evaluation of process quality characteristics using change request data. Results of the study offer insights into the development process of Eclipse. Moreover the study allows assessing applicability and limitations of the proposed approach for the evaluation of process quality

Model-based high cell density cultivation of Rhodospirillum rubrum under respiratory dark conditions

The potential of facultative photosynthetic bacteria as producers of photosynthetic pigments, vitamins, coenzymes and other valuable products has been recognized for decades. However, mass cultivation under photosynthetic conditions is generally inefficient due to the inevitable limitation of light supply when cell densities become very high. The previous development of a new cultivation process for maximal expression of photosynthetic genes under semi-aerobic dark conditions in common bioreactors offers a new perspective for utilizing the facultative photosynthetic bacterium Rhodospirillum rubrum for large-scale applications. Based on this cultivation system, the present study aimed in determining the maximal achievable cell density of R. rubrum in a bioreactor, thereby providing a major milestone on the way to industrial bioprocesses. As a starting point, we focus on aerobic growth due to higher growth rates and more facile process control under this condition, with the option to extend the process by an anaerobic production phase. Process design and optimization were supported by an unstructured computational process model, based on mixed-substrate kinetics. Key parameters for growth and process control were determined in shake-flask experiments or estimated by simulation studies. For fed-batch cultivation, a computer-controlled exponential feed algorithm in combination with a pH-stat element was implemented. As a result, a maximal cell density of 59 g cell dry weight (CDW) L-1 was obtained, representing so far not attainable cell densities for photosynthetic bacteria. The applied exponential fed-batch methodology therefore enters a range which is commonly employed for industrial applications with microbial cells. The biochemical analysis of high cell density cultures revealed metabolic imbalances, such as the accumulation and excretion of tetrapyrrole intermediates of the bacteriochlorophyll biosynthetic pathway John Wiley & Sons, Inc. All Rights Reserved. [accessed March 9, 2010