1
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Magnússon A, Pajander J, Sin G, Stocks S. Determining the linear correlation between dielectric spectroscopy and viable biomass concentration in filamentous fungal fermentations. Biotechnol Lett 2023:10.1007/s10529-023-03384-w. [PMID: 37227599 DOI: 10.1007/s10529-023-03384-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 03/12/2023] [Accepted: 04/21/2023] [Indexed: 05/26/2023]
Abstract
OBJECTIVES Dielectric spectroscopy is commonly used for online monitoring of biomass growth. It is however not utilized for biomass concentration measurements due to poor correlation with Cell Dry Weight (CDW). A calibration methodology is developed that can directly measure viable biomass concentration in a commercial filamentous process using dielectric values, without recourse to independent and challenging viability determinations. RESULTS The methodology is applied to samples from the industrial scale fermentation of a filamentous fungus, Acremonium fusidioides. By mixing fresh and heat-killed samples, linear responses were verified and sample viability could be fitted with the dielectric [Formula: see text] values and total solids concentration. The study included a total of 26 samples across 21 different cultivations, with a legacy at-line viable cell analyzer requiring 2 ml samples, and a modern on-line probe operated at-line with 2 different sample presentation volumes, one compatible with the legacy analyzer, a larger sample volume of 100 ml being compatible with calibration for on-line operation. The linear model provided an [Formula: see text] value of 0.99 between [Formula: see text] and viable biomass across the sample set using either instrument. The difference in ∆C when analyzing 100 mL and 2 mL samples with an in-line probe can be adjusted by a scalar factor of 1.33 within the microbial system used in this study, preserving the linear relation with [Formula: see text] of 0.97. CONCLUSIONS It is possible to directly estimate viable biomass concentrations utilizing dielectric spectroscopy without recourse to extensive and difficult to execute independent viability studies. The same method can be applied to calibrate different instruments to measure viable biomass concentration. Small sample volumes are appropriate as long as the sample volumes are kept consistent.
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Affiliation(s)
- Atli Magnússon
- LEO Pharma A/S, Ballerup, Denmark.
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark.
| | | | - Gürkan Sin
- LEO Pharma A/S, Ballerup, Denmark
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Stuart Stocks
- LEO Pharma A/S, Ballerup, Denmark
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
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2
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Survyla A, Urniezius R, Simutis R. Viable cell estimation of mammalian cells using off-gas-based oxygen uptake rate and aging-specific functional. Talanta 2023; 254:124121. [PMID: 36462281 DOI: 10.1016/j.talanta.2022.124121] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 11/27/2022]
Abstract
This study developed an estimation routine for counting the viable cells in an in vitro fed-batch Chinese hamster ovary cultivation that relies on off-gas information and inlet gas mixture knowledge. We computed the oxygen uptake rate bound to the bioreactor exhaust gas outlet when the inlet gas mixture was stationary. Our mammalian biosynthesis analysis determined the stoichiometric parameters as a function of the average population age. We cross-validated an identical algorithm for mammalian and microbial cultivations and found that the' 99% confidence band of the model generally overlapped with the error bars defined from observations. The resulting RMSE and MAE averages were 0.188 and 0.14e9cells L-1, respectively, when estimating the viable mammalian cell count. The validation for the estimation of total bacterial biomass yielded an MAE and RMSE of 1.78 g L-1 and 2.53 g L-1, respectively. Moreover, our proposed approach provides an online estimation of the average population age for both aerobically cultivated microorganisms.
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Affiliation(s)
- Arnas Survyla
- Department of Automation, Kaunas University of Technology, Studentu 48, LT-51367, Kaunas, Lithuania
| | - Renaldas Urniezius
- Department of Automation, Kaunas University of Technology, Studentu 48, LT-51367, Kaunas, Lithuania.
| | - Rimvydas Simutis
- Department of Automation, Kaunas University of Technology, Studentu 48, LT-51367, Kaunas, Lithuania
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3
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Paiva AR, Pilloni G. Inferring Microbial Biomass Yield and Cell Weight Using Probabilistic Macrochemical Modeling. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:442-454. [PMID: 35038296 DOI: 10.1109/tcbb.2021.3139290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Growth rates and biomass yields are key descriptors used in microbiology studies to understand how microbial species respond to changes in the environment. Of these, biomass yield estimates are typically obtained using cell counts and measurements of the feed substrate. These quantities are perturbed with measurement noise however. Perhaps most crucially, estimating biomass from cell counts, as needed to assess yields, relies on an assumed cell weight. Noise and discrepancies on these assumptions can lead to significant changes in conclusions regarding the microbes' response. This article proposes a methodology to address these challenges using probabilistic macrochemical models of microbial growth. It is shown that a model can be developed to fully use the experimental data, relax assumptions and greatly improve robustness to a priori estimates of the cell weight, and provides uncertainty estimates of key parameters. This methodology is demonstrated in the context of a specific case study and the estimation characteristics are validated in several scenarios using synthetically generated microbial growth data.
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4
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Fernandez-Gatell M, Sanchez-Vila X, Puigagut J. Power assisted MFC-based biosensor for continuous assessment of microbial activity and biomass in freshwater ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 833:155165. [PMID: 35413352 DOI: 10.1016/j.scitotenv.2022.155165] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/16/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
Microbial activity and biomass are important factors that determine nutrient and carbon fluxes in freshwater ecosystems and, therefore are also related to both water quality and climate change induced stressors. This study aimed at assessing the feasibility of a power assisted Microbial Fuel Cell (MFC)-based biosensors for the continuous monitoring of microbial activity and biomass concentrations in saturated freshwater ecosystems. For this purpose, four lab-scale reactors were constructed and operated for 30 weeks. Reactors were fed with four different organic matter concentrations to promote a suite of microbial activity and biomass conditions. The reactors consisted of 3.8 L PVC vessels filled with 23 extractable gravel- sockets, used for microbial activity and biomass assessment, and 1 MFC granular-graphite socket, for biosensing assessment. Microbial activity was determined by the ATP content and the hydrolytic enzymatic activity, and the biomass content was assessed as the volatile solids attached to the gravel. Very significant linear relationships could be established between the parameters studied and the current density produced by the MFC with a very short detection time: 10 min for the ATP content (R2 = 0.88) and 1 h for the enzymatic activity (R2 = 0.78) and biomass (R2 = 0.74). Moreover, the power assisted MFC-based biosensing tool demonstrated to be functional after a long operation time and under a wide range of organic loading conditions. Overall, the results highlight the feasibility to develop a power assisted MFC-based biosensor for on-line monitoring of the microbial activity and biomass of a given ecosystem (either natural or artificial) even in remote locations.
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Affiliation(s)
- Marta Fernandez-Gatell
- GEMMA - Environmental Engineering and Microbiology Research Group, Department of Civil and Environmental Engineering, Universitat Politècnica de Catalunya·BarcelonaTech (UPC), c/ Jordi Girona 1-3, Building D1, 08034 Barcelona, Spain; GHS - Dept. of Civil and Environmental Engineering, UPC, Jordi Girona 1-3, 08034 Barcelona, Spain
| | - Xavier Sanchez-Vila
- GHS - Dept. of Civil and Environmental Engineering, UPC, Jordi Girona 1-3, 08034 Barcelona, Spain; Associated Unit: Hydrogeology Group (UPC-CSIC), Spain
| | - Jaume Puigagut
- GEMMA - Environmental Engineering and Microbiology Research Group, Department of Civil and Environmental Engineering, Universitat Politècnica de Catalunya·BarcelonaTech (UPC), c/ Jordi Girona 1-3, Building D1, 08034 Barcelona, Spain.
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5
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Soft Sensor-Based Monitoring and Efficient Control Strategies of Biomass Concentration for Continuous Cultures of Haloferax mediterranei and Their Application to an Industrial Production Chain. Microorganisms 2019; 7:microorganisms7120648. [PMID: 31817128 PMCID: PMC6956367 DOI: 10.3390/microorganisms7120648] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/21/2019] [Accepted: 12/03/2019] [Indexed: 11/17/2022] Open
Abstract
Continuous bioprocessing using cell retention allows the achievement of high space-time yields for slow-growing organisms such as halophiles. However, the lack of efficient methods for monitoring and control limits the application of biotechnological processes in the industry. The aim of this study was to implement a control and online monitoring strategy for biomass in continuous cultures. For the first time, a feedforward cultivation strategy in a membrane-based cell retention system allowed to control the biomass concentration of the extreme halophilic Haloferax mediterranei at defined levels. Moreover, soft sensor-based biomass estimation allowed reliable monitoring of biomass online. Application of the combined monitoring and control strategy using industrial process water containing formate, phenol, aniline and 4,4′-methylenedianiline could for the first time demonstrate high throughput degradation in this extremophilic bioremediation process, obtaining degradation efficiencies of up to 100%. This process demonstrates the usefulness of continuous halophilic cultures in a circular economy application.
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6
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Tsuchiya K, Cao YY, Kurokawa M, Ashino K, Yomo T, Ying BW. A decay effect of the growth rate associated with genome reduction in Escherichia coli. BMC Microbiol 2018; 18:101. [PMID: 30176803 PMCID: PMC6122737 DOI: 10.1186/s12866-018-1242-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 08/20/2018] [Indexed: 01/21/2023] Open
Abstract
Background Bacterial growth is an important topic in microbiology and of crucial importance to better understand living cells. Bacterial growth dynamics are quantitatively examined using various methods to determine the physical, chemical or biological features of growing populations. Due to methodological differences, the exponential growth rate, which is a parameter that is representative of growth dynamics, should be differentiated. Ignoring such differentiation in the growth analysis might overlook somehow slight but significant changes in cellular features of the growing population. Both experimental and theoretical investigations are required to address these issues. Results This study experimentally verified the differentiation in growth rates attributed to different methodologies, and demonstrated that the most popular method, optical turbidity, led to the determination of a lower growth rate in comparison to the methods based on colony formation and cellular adenosine triphosphate, due to a decay effect of reading OD600 during a population increase. Accordingly, the logistic model, which is commonly applied to the high-throughput growth data reading the OD600, was revised by introducing a new parameter: the decay rate, to compensate for the lowered estimation in growth rates. An improved goodness of fit in comparison to the original model was acquired due to this revision. Applying the modified logistic model to hundreds of growth data acquired from an assortment of Escherichia coli strains carrying the reduced genomes led to an intriguing finding of a correlation between the decay rate and the genome size. The decay effect seemed to be partially attributed to the decrease in cell size accompanied by a population increase and was medium dependent. Conclusions The present study provides not only an improved theoretical tool for the high-throughput studies on bacterial growth dynamics linking with optical turbidity to biological meaning, but also a novel insight of the genome reduction correlated decay effect, which potentially reflects the changing cellular features during population increase. It is valuable for understanding the genome evolution and the fitness increase in microbial life. Electronic supplementary material The online version of this article (10.1186/s12866-018-1242-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kouhei Tsuchiya
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki, 305-8572, Japan
| | - Yang-Yang Cao
- Institute of Biology and Information Science, East China Normal University, 3663 Zhongshan Road (N), Shanghai, 200062, China
| | - Masaomi Kurokawa
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki, 305-8572, Japan
| | - Kazuha Ashino
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki, 305-8572, Japan
| | - Tetsuya Yomo
- Institute of Biology and Information Science, East China Normal University, 3663 Zhongshan Road (N), Shanghai, 200062, China
| | - Bei-Wen Ying
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki, 305-8572, Japan.
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7
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Estimation of plasmid concentration in batch culture of Escherichia coli DH5α via simple state observer. CHEMICAL PAPERS 2018. [DOI: 10.1007/s11696-018-0478-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Abstract
Bacterial growth is a central concept in the development of modern microbial physiology, as well as in the investigation of cellular dynamics at the systems level. Recent studies have reported correlations between bacterial growth and genome-wide events, such as genome reduction and transcriptome reorganization. Correctly analyzing bacterial growth is crucial for understanding the growth-dependent coordination of gene functions and cellular components. Accordingly, the precise quantitative evaluation of bacterial growth in a high-throughput manner is required. Emerging technological developments offer new experimental tools that allow updates of the methods used for studying bacterial growth. The protocol introduced here employs a microplate reader with a highly optimized experimental procedure for the reproducible and precise evaluation of bacterial growth. This protocol was used to evaluate the growth of several previously described Escherichia coli strains. The main steps of the protocol are as follows: the preparation of a large number of cell stocks in small vials for repeated tests with reproducible results, the use of 96-well plates for high-throughput growth evaluation, and the manual calculation of two major parameters (i.e., maximal growth rate and population density) representing the growth dynamics. In comparison to the traditional colony-forming unit (CFU) assay, which counts the cells that are cultured in glass tubes over time on agar plates, the present method is more efficient and provides more detailed temporal records of growth changes, but has a stricter detection limit at low population densities. In summary, the described method is advantageous for the precise and reproducible high-throughput analysis of bacterial growth, which can be used to draw conceptual conclusions or to make theoretical observations.
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Affiliation(s)
- Masaomi Kurokawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Bei-Wen Ying
- Graduate School of Life and Environmental Sciences, University of Tsukuba; Institute of Biology and Information Science, East China Normal University;
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9
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Oyama LB, Crochet JA, Edwards JE, Girdwood SE, Cookson AR, Fernandez-Fuentes N, Hilpert K, Golyshin PN, Golyshina OV, Privé F, Hess M, Mantovani HC, Creevey CJ, Huws SA. Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalis. Front Chem 2017; 5:51. [PMID: 28748180 PMCID: PMC5506224 DOI: 10.3389/fchem.2017.00051] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/27/2017] [Indexed: 11/14/2022] Open
Abstract
Antimicrobial peptides (AMPs) are gaining popularity as alternatives for treatment of bacterial infections and recent advances in omics technologies provide new platforms for AMP discovery. We sought to determine the antibacterial activity of a novel antimicrobial peptide, buwchitin, against Enterococcus faecalis. Buwchitin was identified from a rumen bacterial metagenome library, cloned, expressed and purified. The antimicrobial activity of the recombinant peptide was assessed using a broth microdilution susceptibility assay to determine the peptide's killing kinetics against selected bacterial strains. The killing mechanism of buwchitin was investigated further by monitoring its ability to cause membrane depolarization (diSC3(5) method) and morphological changes in E. faecalis cells. Transmission electron micrographs of buwchitin treated E. faecalis cells showed intact outer membranes with blebbing, but no major damaging effects and cell morphology changes. Buwchitin had negligible cytotoxicity against defibrinated sheep erythrocytes. Although no significant membrane leakage and depolarization was observed, buwchitin at minimum inhibitory concentration (MIC) was bacteriostatic against E. faecalis cells and inhibited growth in vitro by 70% when compared to untreated cells. These findings suggest that buwchitin, a rumen derived peptide, has potential for antimicrobial activity against E. faecalis.
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Affiliation(s)
- Linda B Oyama
- Institute of Biological Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Jean-Adrien Crochet
- Institute of Biological Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Joan E Edwards
- Institute of Biological Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Susan E Girdwood
- Institute of Biological Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Alan R Cookson
- Institute of Biological Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Narcis Fernandez-Fuentes
- Institute of Biological Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Kai Hilpert
- Institute of Infection and Immunity, St George's University of LondonLondon, United Kingdom
| | - Peter N Golyshin
- School of Biological Sciences, Bangor UniversityBangor, United Kingdom
| | - Olga V Golyshina
- School of Biological Sciences, Bangor UniversityBangor, United Kingdom
| | - Florence Privé
- Institute of Biological Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Matthias Hess
- College of Agricultural and Environmental Sciences, University of California, DavisDavis, CA, United States
| | | | - Christopher J Creevey
- Institute of Biological Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Sharon A Huws
- Medical Biology Centre, School of Biological Sciences, Queen's University BelfastBelfast, United Kingdom
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10
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Bruder S, Reifenrath M, Thomik T, Boles E, Herzog K. Parallelised online biomass monitoring in shake flasks enables efficient strain and carbon source dependent growth characterisation of Saccharomyces cerevisiae. Microb Cell Fact 2016; 15:127. [PMID: 27455954 PMCID: PMC4960845 DOI: 10.1186/s12934-016-0526-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 07/18/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Baker's yeast, Saccharomyces cerevisiae, as one of the most often used workhorses in biotechnology has been developed into a huge family of application optimised strains in the last decades. Increasing numbers of strains render their characterisation highly challenging, even with the simple methods of growth-based analytics. Here we present a new sensor system for the automated, non-invasive and parallelisable monitoring of biomass in continuously shaken shake flask cultures, called CGQ ("cell growth quantifier"). The CGQ implements a dynamic approach of backscattered light measurement, allowing for efficient and accurate growth-based strain characterisation, as exemplarily demonstrated for the four most commonly used laboratory and industrial yeast strains, BY4741, W303-1A, CEN.PK2-1C and Ethanol Red. RESULTS Growth experiments revealed distinct carbon source utilisation differences between the investigated S. cerevisiae strains. Phenomena such as diauxic shifts, morphological changes and oxygen limitations were clearly observable in the growth curves. A strictly monotonic non-linear correlation of OD600 and the CGQ's backscattered light intensities was found, with strain-to-strain as well as growth-phase related differences. The CGQ measurements showed high resolution, sensitivity and smoothness even below an OD600 of 0.2 and were furthermore characterised by low background noise and signal drift in combination with high reproducibility. CONCLUSIONS With the CGQ, shake flask fermentations can be automatically monitored regarding biomass and growth rates with high resolution and parallelisation. This makes the CGQ a valuable tool for growth-based strain characterisation and development. The exceptionally high resolution allows for the identification of distinct metabolic differences and shifts as well as for morphologic changes. Applications that will benefit from that kind of automatized biomass monitoring include, amongst many others, the characterization of deregulated native or integrated heterologous pathways, the fast detection of co-fermentation as well as the realisation of rational and growth-data driven evolutionary engineering approaches.
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Affiliation(s)
- Stefan Bruder
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Mara Reifenrath
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Thomas Thomik
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Eckhard Boles
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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11
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Cañete-Rodríguez A, Santos-Dueñas I, Jiménez-Hornero J, Torija-Martínez M, Mas A, García-García I. An approach for estimating the maximum specific growth rate of Gluconobacter japonicus in strawberry purée without cell concentration data. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2015.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Better One-Eyed than Blind--Challenges and Opportunities of Biomass Measurement During Solid-State Fermentation of Basidiomycetes. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 149:223-52. [PMID: 25860889 DOI: 10.1007/10_2014_300] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Filamentous fungi, especially basidiomycetes, produce a wide range of metabolites, many of which have potential biotechnological and industrial applications. Solid-state fermentation (SSF) is very suitable for the cultivation of basidiomycetes since it mimics the natural habitat of these fungi. Some of the major advantages of SSF are the robustness of the process, the use of low-cost residual materials as substrates, and the reduced usage of water. However, monitoring key variables is difficult, which makes process control a challenge. Specifically, it is very difficult to determine the biomass during SSF process involving basidiomycetes. This is problematic, as the biomass is normally a key variable in mass and energy balance equations. Further, the success of fungal SSF processes is often evaluated, in part, based on the growth of the fungus. Direct determination of the dry weight of biomass is impossible and indirect quantification techniques must be used. Over the years, various determination techniques have been developed for the quantification of fungal biomass in SSF processes. The current review gives an overview of various direct and indirect biomass determination methods, discussing their advantages and disadvantages.
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13
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Ying BW, Honda T, Tsuru S, Seno S, Matsuda H, Kazuta Y, Yomo T. Evolutionary Consequence of a Trade-Off between Growth and Maintenance along with Ribosomal Damages. PLoS One 2015; 10:e0135639. [PMID: 26292224 PMCID: PMC4546238 DOI: 10.1371/journal.pone.0135639] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 07/24/2015] [Indexed: 12/15/2022] Open
Abstract
Microorganisms in nature are constantly subjected to a limited availability of resources and experience repeated starvation and nutrition. Therefore, microbial life may evolve for both growth fitness and sustainability. By contrast, experimental evolution, as a powerful approach to investigate microbial evolutionary strategies, often targets the increased growth fitness in controlled, steady-state conditions. Here, we address evolutionary changes balanced between growth and maintenance while taking nutritional fluctuations into account. We performed a 290-day-long evolution experiment with a histidine-requiring Escherichia coli strain that encountered repeated histidine-rich and histidine-starved conditions. The cells that experienced seven rounds of starvation and re-feed grew more sustainably under prolonged starvation but dramatically lost growth fitness under rich conditions. The improved sustainability arose from the evolved capability to use a trace amount of histidine for cell propagation. The reduced growth rate was attributed to mutations genetically disturbing the translation machinery, that is, the ribosome, ultimately slowing protein translation. This study provides the experimental demonstration of slow growth accompanied by an enhanced affinity to resources as an evolutionary adaptation to oscillated environments and verifies that it is possible to evolve for reduced growth fitness. Growth economics favored for population increase under extreme resource limitations is most likely a common survival strategy adopted by natural microbes.
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Affiliation(s)
- Bei-Wen Ying
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305–8572, Japan
| | - Tomoya Honda
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093, United States of America
| | - Saburo Tsuru
- Graduate School of Information Science and Technology, Osaka University, 1–5 Yamadaoka, Suita, Osaka, 565–0871, Japan
| | - Shigeto Seno
- Graduate School of Information Science and Technology, Osaka University, 1–5 Yamadaoka, Suita, Osaka, 565–0871, Japan
| | - Hideo Matsuda
- Graduate School of Information Science and Technology, Osaka University, 1–5 Yamadaoka, Suita, Osaka, 565–0871, Japan
| | - Yasuaki Kazuta
- ERATO, JST, 1–5 Yamadaoka, Suita, Osaka, 565–0871, Japan
| | - Tetsuya Yomo
- Graduate School of Information Science and Technology, Osaka University, 1–5 Yamadaoka, Suita, Osaka, 565–0871, Japan
- ERATO, JST, 1–5 Yamadaoka, Suita, Osaka, 565–0871, Japan
- Graduate School of Frontier Biosciences, Osaka University, 1–5 Yamadaoka, Suita, Osaka, 565–0871, Japan
- * E-mail:
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14
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Simon LL, Pataki H, Marosi G, Meemken F, Hungerbühler K, Baiker A, Tummala S, Glennon B, Kuentz M, Steele G, Kramer HJM, Rydzak JW, Chen Z, Morris J, Kjell F, Singh R, Gani R, Gernaey KV, Louhi-Kultanen M, O’Reilly J, Sandler N, Antikainen O, Yliruusi J, Frohberg P, Ulrich J, Braatz RD, Leyssens T, von Stosch M, Oliveira R, Tan RBH, Wu H, Khan M, O’Grady D, Pandey A, Westra R, Delle-Case E, Pape D, Angelosante D, Maret Y, Steiger O, Lenner M, Abbou-Oucherif K, Nagy ZK, Litster JD, Kamaraju VK, Chiu MS. Assessment of Recent Process Analytical Technology (PAT) Trends: A Multiauthor Review. Org Process Res Dev 2015. [DOI: 10.1021/op500261y] [Citation(s) in RCA: 269] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | - Hajnalka Pataki
- Department
of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - György Marosi
- Department
of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Fabian Meemken
- Department
of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg
1, 8093 Zürich, Switzerland
| | - Konrad Hungerbühler
- Department
of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg
1, 8093 Zürich, Switzerland
| | - Alfons Baiker
- Department
of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg
1, 8093 Zürich, Switzerland
| | - Srinivas Tummala
- Chemical
Development, Bristol-Myers Squibb Company, One Squibb Dr, New Brunswick, New Jersey 08903, United States
| | - Brian Glennon
- Synthesis
and Solid State Pharmaceutical Centre, School of Chemical and Bioprocess
Engineering, University College Dublin, Belfield, Dublin 4, Ireland
- APC Ltd, Belfield Innovation
Park, Dublin 4, Ireland
| | - Martin Kuentz
- School of Life
Sciences, Institute of Pharma Technology, University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, 4132 Muttenz, Switzerland
| | - Gerry Steele
- PharmaCryst Consulting
Ltd., Loughborough, Leicestershire LE11 3HN, U.K
| | - Herman J. M. Kramer
- Intensified Reaction & Separation Systems, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft, The Netherlands
| | - James W. Rydzak
- GlaxoSmithKline Pharmaceuticals, 709 Swedeland Rd, King of
Prussia, Pennsylvania 19406, United States
| | - Zengping Chen
- State Key
Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry
and Chemical Engineering, Hunan University, Changsha, Hunan 410082, PR China
| | - Julian Morris
- Centre for Process Analytics & Control Technology, School of Chemical Engineering & Advanced Materials, Newcastle University, Newcastle upon Tyne, Tyne and Wear NE17RU, U.K
| | - Francois Kjell
- Siemens nv/sa,
Industry
Automation − SIPAT Industry Software, Marie Curie Square 30, 1070 Brussels, Belgium
| | - Ravendra Singh
- CAPEC-PROCESS,
Department of Chemical and Biochemical Engineering, Technical University of Denmark (DTU), Building 229, DK-2800 Lyngby, Denmark
| | - Rafiqul Gani
- CAPEC-PROCESS,
Department of Chemical and Biochemical Engineering, Technical University of Denmark (DTU), Building 229, DK-2800 Lyngby, Denmark
| | - Krist V. Gernaey
- CAPEC-PROCESS,
Department of Chemical and Biochemical Engineering, Technical University of Denmark (DTU), Building 229, DK-2800 Lyngby, Denmark
| | - Marjatta Louhi-Kultanen
- Department
of Chemical Technology, Lappeenranta University of Technology, P.O. Box 20, FI-53851 Lappeenranta, Finland
| | - John O’Reilly
- Roche Ireland
Limited, Clarecastle, Co. Clare, Ireland
| | - Niklas Sandler
- Pharmaceutical
Sciences Laboratory, Department of Biosciences, Abo Akademi University, Artillerigatan 6, 20520 Turku, Finland
| | - Osmo Antikainen
- Division
of Pharmaceutical Technology, Faculty of Pharmacy, University of Helsinki, Yliopistonkatu 4, 00100 Helsinki, Finland
| | - Jouko Yliruusi
- Division
of Pharmaceutical Technology, Faculty of Pharmacy, University of Helsinki, Yliopistonkatu 4, 00100 Helsinki, Finland
| | - Patrick Frohberg
- Center of
Engineering Science, Thermal Process Engineering, Martin Luther University Halle-Wittenberg, D-06099 Halle (Saale), Germany
| | - Joachim Ulrich
- Center of
Engineering Science, Thermal Process Engineering, Martin Luther University Halle-Wittenberg, D-06099 Halle (Saale), Germany
| | - Richard D. Braatz
- Massachusetts Institute
of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Tom Leyssens
- Institute
of Condensed Matter and Nanosciences, Université Catholique de Louvain, Place Louis Pasteur 1, 1348 Louvain-la-Neuve, Belgium
| | - Moritz von Stosch
- REQUIMTE
- Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 1099-085 Caparica, Portugal
- HybPAT, Caparica, Portugal
| | - Rui Oliveira
- REQUIMTE
- Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 1099-085 Caparica, Portugal
- HybPAT, Caparica, Portugal
| | - Reginald B. H. Tan
- Institute
of Chemical and Engineering Sciences, A*Star, 1 Pesek Road, Singapore 627833
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576
| | - Huiquan Wu
- Division
of Product Quality Research, Office of Testing and Research, Office
of Pharmaceutical Science, Center for Drug Evaluation and Research, US Food and Drug Administration (FDA), Silver Spring, Maryland 20993, United States
| | - Mansoor Khan
- Division
of Product Quality Research, Office of Testing and Research, Office
of Pharmaceutical Science, Center for Drug Evaluation and Research, US Food and Drug Administration (FDA), Silver Spring, Maryland 20993, United States
| | - Des O’Grady
- Mettler Toledo
AutoChem, 7075 Samuel Morse Drive, Columbia, Maryland 20146, United States
| | - Anjan Pandey
- Mettler Toledo
AutoChem, 7075 Samuel Morse Drive, Columbia, Maryland 20146, United States
| | - Remko Westra
- FMC Technologies B.V., Delta 101, 6825 MN Arnhem, The Netherlands
| | - Emmanuel Delle-Case
- University of Tulsa, 800 South Tucker
Drive, Tulsa, Oklahoma 74104, United States
| | - Detlef Pape
- ABB Corporate Research Center, Segelhofstrasse
1K, 5405, Dättwil, Baden, Switzerland
| | - Daniele Angelosante
- ABB Corporate Research Center, Segelhofstrasse
1K, 5405, Dättwil, Baden, Switzerland
| | - Yannick Maret
- ABB Corporate Research Center, Segelhofstrasse
1K, 5405, Dättwil, Baden, Switzerland
| | - Olivier Steiger
- ABB Corporate Research Center, Segelhofstrasse
1K, 5405, Dättwil, Baden, Switzerland
| | - Miklós Lenner
- ABB Corporate Research Center, Segelhofstrasse
1K, 5405, Dättwil, Baden, Switzerland
| | - Kaoutar Abbou-Oucherif
- School of
Chemical Engineering, Purdue University, West Lafayette, Indiana 47906, United States
| | - Zoltan K. Nagy
- School of
Chemical Engineering, Purdue University, West Lafayette, Indiana 47906, United States
- Chemical
Engineering Department, Loughborough University, Loughborough, LE11 3TU, U.K
| | - James D. Litster
- School of
Chemical Engineering, Purdue University, West Lafayette, Indiana 47906, United States
| | - Vamsi Krishna Kamaraju
- Synthesis
and Solid State Pharmaceutical Centre, School of Chemical and Bioprocess
Engineering, University College Dublin, Belfield, Dublin 4, Ireland
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576
| | - Min-Sen Chiu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576
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15
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Steudler S, Böhmer U, Weber J, Bley T. Biomass measurement by flow cytometry during solid-state fermentation of basidiomycetes. Cytometry A 2014; 87:176-88. [DOI: 10.1002/cyto.a.22592] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 10/24/2014] [Accepted: 10/28/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Susanne Steudler
- Institut für Lebensmittel- und Bioverfahrenstechnik, Technische Universität Dresden; Dresden Germany
| | - Ulrike Böhmer
- Gesellschaft für Wissens- und Technologietransfer-TU Dresden GmbH, (GWT-TUD GmbH); Dresden Germany
| | - Jost Weber
- Institut für Lebensmittel- und Bioverfahrenstechnik, Technische Universität Dresden; Dresden Germany
| | - Thomas Bley
- Institut für Lebensmittel- und Bioverfahrenstechnik, Technische Universität Dresden; Dresden Germany
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16
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Ude C, Schmidt-Hager J, Findeis M, John GT, Scheper T, Beutel S. Application of an online-biomass sensor in an optical multisensory platform prototype for growth monitoring of biotechnical relevant microorganism and cell lines in single-use shake flasks. SENSORS (BASEL, SWITZERLAND) 2014; 14:17390-405. [PMID: 25232914 PMCID: PMC4208230 DOI: 10.3390/s140917390] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/02/2014] [Accepted: 09/03/2014] [Indexed: 11/29/2022]
Abstract
In the context of this work we evaluated a multisensory, noninvasive prototype platform for shake flask cultivations by monitoring three basic parameters (pH, pO2 and biomass). The focus lies on the evaluation of the biomass sensor based on backward light scattering. The application spectrum was expanded to four new organisms in addition to E. coli K12 and S. cerevisiae [1]. It could be shown that the sensor is appropriate for a wide range of standard microorganisms, e.g., L. zeae, K. pastoris, A. niger and CHO-K1. The biomass sensor signal could successfully be correlated and calibrated with well-known measurement methods like OD600, cell dry weight (CDW) and cell concentration. Logarithmic and Bleasdale-Nelder derived functions were adequate for data fitting. Measurements at low cell concentrations proved to be critical in terms of a high signal to noise ratio, but the integration of a custom made light shade in the shake flask improved these measurements significantly. This sensor based measurement method has a high potential to initiate a new generation of online bioprocess monitoring. Metabolic studies will particularly benefit from the multisensory data acquisition. The sensor is already used in labscale experiments for shake flask cultivations.
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Affiliation(s)
- Christian Ude
- Leibniz University of Hanover, Institute of Technical Chemistry, Callinstr. 5, 30167 Hannover, Germany; E-Mails: (C.U.); (J.S.-H.), (T.S.)
| | - Jörg Schmidt-Hager
- Leibniz University of Hanover, Institute of Technical Chemistry, Callinstr. 5, 30167 Hannover, Germany; E-Mails: (C.U.); (J.S.-H.), (T.S.)
| | - Michael Findeis
- PreSens Precision Sensing GmbH, Josef-Engert-Str. 11, 93053 Regensburg, Germany; E-Mails: (M.F.); (G.T.J.)
| | - Gernot Thomas John
- PreSens Precision Sensing GmbH, Josef-Engert-Str. 11, 93053 Regensburg, Germany; E-Mails: (M.F.); (G.T.J.)
| | - Thomas Scheper
- Leibniz University of Hanover, Institute of Technical Chemistry, Callinstr. 5, 30167 Hannover, Germany; E-Mails: (C.U.); (J.S.-H.), (T.S.)
| | - Sascha Beutel
- Leibniz University of Hanover, Institute of Technical Chemistry, Callinstr. 5, 30167 Hannover, Germany; E-Mails: (C.U.); (J.S.-H.), (T.S.)
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17
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Schmidt-Hager J, Ude C, Findeis M, John GT, Scheper T, Beutel S. Noninvasive online biomass detector system for cultivation in shake flasks. Eng Life Sci 2014. [DOI: 10.1002/elsc.201400026] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Jörg Schmidt-Hager
- Institute of Technical Chemistry; Leibniz University of Hannover; Hannover Germany
| | - Christian Ude
- Institute of Technical Chemistry; Leibniz University of Hannover; Hannover Germany
| | | | | | - Thomas Scheper
- Institute of Technical Chemistry; Leibniz University of Hannover; Hannover Germany
| | - Sascha Beutel
- Institute of Technical Chemistry; Leibniz University of Hannover; Hannover Germany
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18
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Sarrafzadeh MH, Schorr-Galindo S, La HJ, Oh HM. Aeration effects on metabolic events during sporulation of Bacillus thuringiensis. J Microbiol 2014; 52:597-603. [PMID: 24972809 DOI: 10.1007/s12275-014-3547-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 04/15/2014] [Accepted: 04/19/2014] [Indexed: 11/28/2022]
Abstract
The metabolism of Bacillus thuringiensis during its sporulation process was investigated under different concentrations of oxygen. At the beginning of sporulation, the aeration conditions were regulated to obtain different oxygen transfer rates (OTR) in four separate fermentations, representing interrupted, limited, non-limited, and saturated oxygenation, respectively. A higher OTR resulted in a higher pH, up to about 9 in the case of saturated oxygenation, while the interrupted oxygenation resulted in a significantly acidic culture. In contrast, the absence of oxygen resulted in rapid sporangia lysis and caused acidification of the medium, indicating a distinctly different sporangia composition and different metabolism. The bacterium also showed different CO2 production rates during sporulation, although a maximum point was observed in every case.With a higher OTR, the maximal value was observed after a longer time and at a lower value (40, 26, and 13 mmol/L/h for limited, non-limited, and saturated cases, respectively). Despite the exhaustion of glucose prior to the sporulation phase, the interrupted oxygenation resulted in acetate, lactate, and citrate in the medium with a maximum concentration of 4.8, 1.3, and 5.0 g/L, respectively. Notwithstanding, while the metabolic events differed visibly in the absence of oxygen, once sporulation was triggered, it was completed, even in the case of an interrupted oxygen supply.
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Affiliation(s)
- Mohammad H Sarrafzadeh
- School of Chemical Engineering, College of Engineering, University of Tehran, Tehran, P.O. Box 11155-4563, Iran
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19
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Chioccioli M, Hankamer B, Ross IL. Flow cytometry pulse width data enables rapid and sensitive estimation of biomass dry weight in the microalgae Chlamydomonas reinhardtii and Chlorella vulgaris. PLoS One 2014; 9:e97269. [PMID: 24832156 PMCID: PMC4022489 DOI: 10.1371/journal.pone.0097269] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 04/16/2014] [Indexed: 11/19/2022] Open
Abstract
Dry weight biomass is an important parameter in algaculture. Direct measurement requires weighing milligram quantities of dried biomass, which is problematic for small volume systems containing few cells, such as laboratory studies and high throughput assays in microwell plates. In these cases indirect methods must be used, inducing measurement artefacts which vary in severity with the cell type and conditions employed. Here, we utilise flow cytometry pulse width data for the estimation of cell density and biomass, using Chlorella vulgaris and Chlamydomonas reinhardtii as model algae and compare it to optical density methods. Measurement of cell concentration by flow cytometry was shown to be more sensitive than optical density at 750 nm (OD750) for monitoring culture growth. However, neither cell concentration nor optical density correlates well to biomass when growth conditions vary. Compared to the growth of C. vulgaris in TAP (tris-acetate-phosphate) medium, cells grown in TAP + glucose displayed a slowed cell division rate and a 2-fold increased dry biomass accumulation compared to growth without glucose. This was accompanied by increased cellular volume. Laser scattering characteristics during flow cytometry were used to estimate cell diameters and it was shown that an empirical but nonlinear relationship could be shown between flow cytometric pulse width and dry weight biomass per cell. This relationship could be linearised by the use of hypertonic conditions (1 M NaCl) to dehydrate the cells, as shown by density gradient centrifugation. Flow cytometry for biomass estimation is easy to perform, sensitive and offers more comprehensive information than optical density measurements. In addition, periodic flow cytometry measurements can be used to calibrate OD750 measurements for both convenience and accuracy. This approach is particularly useful for small samples and where cellular characteristics, especially cell size, are expected to vary during growth.
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Affiliation(s)
- Maurizio Chioccioli
- Institute for Molecular Biosciences (IMB), The University of Queensland, Brisbane, Queensland, Australia
| | - Ben Hankamer
- Institute for Molecular Biosciences (IMB), The University of Queensland, Brisbane, Queensland, Australia
| | - Ian L. Ross
- Institute for Molecular Biosciences (IMB), The University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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20
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Kokina A, Kibilds J, Liepins J. Adenine auxotrophy--be aware: some effects of adenine auxotrophy in Saccharomyces cerevisiae strain W303-1A. FEMS Yeast Res 2014; 14:697-707. [PMID: 24661329 DOI: 10.1111/1567-1364.12154] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 02/24/2014] [Accepted: 03/18/2014] [Indexed: 11/27/2022] Open
Abstract
Adenine auxotrophy is a commonly used genetic marker in haploid yeast strains. Strain W303-1A, which carries the ade2-1 mutation, is widely used in physiological and genetic research. Yeast extract-based rich medium contains a low level of adenine, so that adenine is often depleted before glucose. This could affect the cell physiology of adenine auxotrophs grown in rich medium. The aim of our study was to assess the effects of adenine auxotrophy on cell morphology and stress physiology. Our results show that adenine depletion halts cell division, but that culture optical density continues to increase due to cell swelling. Accumulation of trehalose and a coincident 10-fold increase in desiccation stress tolerance is observed in adenine auxotrophs after adenine depletion, when compared to prototrophs. Under adenine starvation, long-term survival of W303-1A is lower than during carbon starvation, but higher than during leucine starvation. We observed drastic adenine-dependent changes in cell stress physiology, suggesting that results may be biased when adenine auxotrophs are grown in rich media without adenine supplementation.
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Affiliation(s)
- Agnese Kokina
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
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21
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Dong D, Sutaria S, Hwangbo JY, Chen P. A simple and rapid method to isolate purer M13 phage by isoelectric precipitation. Appl Microbiol Biotechnol 2013; 97:8023-9. [PMID: 23807666 DOI: 10.1007/s00253-013-5049-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/06/2013] [Accepted: 06/09/2013] [Indexed: 11/25/2022]
Abstract
M13 virus (phage) has been extensively used in phage display technology and nanomaterial templating. Our research aimed to use M13 phage to template sulfur nanoparticles for making lithium ion batteries. Traditional methods for harvesting M13 phage from Escherichia coli employ polyethylene glycol (PEG)-based precipitation, and the yield is usually measured by plaque counting. With this method, PEG residue is present in the M13 phage pellet and is difficult to eliminate. To resolve this issue, a method based on isoelectric precipitation was introduced and tested. The isoelectric method resulted in the production of purer phage with a higher yield, compared to the traditional PEG-based method. There is no significant variation in infectivity of the phage prepared using isoelectric precipitation, and the dynamic light scattering data indirectly prove that the phage structure is not damaged by pH adjustment. To maximize phage production, a dry-weight yield curve of M13 phage for various culture times was produced. The yield curve is proportional to the growth curve of E. coli. On a 200-mL culture scale, 0.2 g L(-1) M13 phage (dry-weight) was produced by the isoelectric precipitation method.
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Affiliation(s)
- Dexian Dong
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
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22
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Wang Z, Guo X, Jia L, Ding Y. Improved synchronous light scattering method for measuring baker's yeast biomass using thickened suspensions. World J Microbiol Biotechnol 2013; 29:1531-6. [PMID: 23529355 DOI: 10.1007/s11274-013-1315-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 03/09/2013] [Indexed: 10/27/2022]
Abstract
Measuring yeast biomass is important in the processes of microbial fermentations. It has been demonstrated that synchronous light scattering (SLS) signals could be applied for the quantification of model bioparticles such as Saccharomyces cerevisiae. In this study, an improved synchronous light scattering method was developed for yeast biomass estimation. The settlement of yeast cells during SLS signals measuring process was studied, and hydrolysis anionic polyacrylamide was added into yeast suspensions to increase the stability of the cells in liquid environment. By simultaneously scanning both the excitation and emission monochromators of a common spectrofluorometer with same starting excitation and emission wavelength (namely, ∆λ = 0), the SLS intensity was found to be proportional to the yeast concentration in the range from 0 to 4.9 × 10(6) cell/mL (R (2) = 0.9907), the detection limit is 8.1 × 10(3) cell/mL. The developed method exhibited good stability and sensitivity in the recovery test and growth curve drawing process, demonstrating the potential of the method in practical application of biomass estimation.
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Affiliation(s)
- Zhen Wang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, China
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23
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24
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Sonnleitner B. Automated measurement and monitoring of bioprocesses: key elements of the M(3)C strategy. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012. [PMID: 23179291 DOI: 10.1007/10_2012_173] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
The state-of-routine monitoring items established in the bioprocess industry as well as some important state-of-the-art methods are briefly described and the potential pitfalls discussed. Among those are physical and chemical variables such as temperature, pressure, weight, volume, mass and volumetric flow rates, pH, redox potential, gas partial pressures in the liquid and molar fractions in the gas phase, infrared spectral analysis of the liquid phase, and calorimetry over an entire reactor. Classical as well as new optical versions are addressed. Biomass and bio-activity monitoring (as opposed to "measurement") via turbidity, permittivity, in situ microscopy, and fluorescence are critically analyzed. Some new(er) instrumental analytical tools, interfaced to bioprocesses, are explained. Among those are chromatographic methods, mass spectrometry, flow and sequential injection analyses, field flow fractionation, capillary electrophoresis, and flow cytometry. This chapter surveys the principles of monitoring rather than compiling instruments.
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Affiliation(s)
- Bernhard Sonnleitner
- Institute for Chemistry and Biological Chemistry (ICBC), Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 29, CH-8820, Waedenswil, Switzerland,
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25
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Barrigón JM, Ramon R, Rocha I, Valero F, Ferreira EC, Montesinos JL. State and specific growth estimation in heterologous protein production by Pichia pastoris. AIChE J 2011. [DOI: 10.1002/aic.12810] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Introducing process analytical technology (PAT) in filamentous cultivation process development: comparison of advanced online sensors for biomass measurement. J Ind Microbiol Biotechnol 2011; 38:1679-90. [DOI: 10.1007/s10295-011-0957-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 03/09/2011] [Indexed: 12/24/2022]
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27
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Burdíková Z, Capek M, Ostašov P, Machač J, Pelc R, Mitchell EAD, Kubínová L. Testate amoebae examined by confocal and two-photon microscopy: implications for taxonomy and ecophysiology. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2010; 16:735-746. [PMID: 21092357 DOI: 10.1017/s1431927610094031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Testate amoebae (TA) are a group of free-living protozoa, important in ecology and paleoecology. Testate amoebae taxonomy is mainly based on the morphological features of the shell, as examined by means of light microscopy or (environmental) scanning electron microscopy (SEM/ESEM). We explored the potential applications of confocal laser scanning microscopy (CLSM), two photon excitation microscopy (TPEM), phase contrast, differential interference contrast (DIC Nomarski), and polarization microscopy to visualize TA shells and inner structures of living cells, which is not possible by SEM or environmental SEM. Images captured by CLSM and TPEM were utilized to create three-dimensional (3D) visualizations and to evaluate biovolume inside the shell by stereological methods, to assess the function of TA in ecosystems. This approach broadens the understanding of TA cell and shell morphology, and inner structures including organelles and endosymbionts, with potential implications in taxonomy and ecophysiology.
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Affiliation(s)
- Zuzana Burdíková
- Institute of Physiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-14220 Prague 4, Czech Republic.
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28
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29
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Bot CT, Prodan C. Quantifying the membrane potential during E. coli growth stages. Biophys Chem 2009; 146:133-7. [PMID: 20031298 DOI: 10.1016/j.bpc.2009.11.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2009] [Revised: 11/20/2009] [Accepted: 11/20/2009] [Indexed: 12/01/2022]
Abstract
The presence of the resting membrane potential has a strong effect on the dielectric behavior of cell suspensions. Using this observation and a well-established theoretical model, the low frequency dielectric dispersion curves of E. coli cell suspensions are de-convoluted to obtain the resting membrane potential of E. coli cells at various growth stages. Four regions of the exponential growth stage are investigated and the measurements indicate that the membrane depolarizes from -220mV in the early exponential phase to -140mV in the late exponential phase. The conductivity of the cell suspension is also found to decrease as the cells progress from the early to the late exponential phases.
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Affiliation(s)
- Corina Teodora Bot
- New Jersey Institute of Technology, Physics Department, Newark, 07102, USA.
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30
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Vries D, Verheijen PJ, den Dekker AJ. Identification. Hybrid system modeling and identification of cell biology systems: perspectives and challenges. ACTA ACUST UNITED AC 2009. [DOI: 10.3182/20090706-3-fr-2004.00038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Ko CL, Wang FS. On-line estimation of biomass and intracellular protein for recombinant Escherichia coli cultivated in batch and fed-batch modes. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.jcice.2007.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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32
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Charrière F, Pavillon N, Colomb T, Depeursinge C, Heger TJ, Mitchell EAD, Marquet P, Rappaz B. Living specimen tomography by digital holographic microscopy: morphometry of testate amoeba. OPTICS EXPRESS 2006; 14:7005-13. [PMID: 19529071 DOI: 10.1364/oe.14.007005] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
This paper presents an optical diffraction tomography technique based on digital holographic microscopy. Quantitative 2-dimensional phase images are acquired for regularly-spaced angular positions of the specimen covering a total angle of pi, allowing to built 3-dimensional quantitative refractive index distributions by an inverse Radon transform. A 20x magnification allows a resolution better than 3 microm in all three dimensions, with accuracy better than 0.01 for the refractive index measurements. This technique is for the first time to our knowledge applied to living specimen (testate amoeba, Protista). Morphometric measurements are extracted from the tomographic reconstructions, showing that the commonly used method for testate amoeba biovolume evaluation leads to systematic under evaluations by about 50%.
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Affiliation(s)
- Florian Charrière
- Ecole Polytechnique Fédérale de Lausanne, Imaging and Applied Optics Institute, CH-1015 Lausanne, Switzerland.
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