Modeling the dynamics of E. coli populations in the three-dimensional turbulent field of a stirred-tank bioreactor—A structured–segregated approach

2006 ◽  
Vol 61 (14) ◽  
pp. 4783-4797 ◽  
Author(s):  
Alexei Lapin ◽  
Joachim Schmid ◽  
Matthias Reuss
Keyword(s):  
Three Dimensional ◽  
Stirred Tank ◽  
Stirred Tank Bioreactor ◽  
E Coli ◽  
Turbulent Field

Kinetics and modelling of batch fermentation for the production of organic solvent tolerant and thermostable lipase by recombinant E. coli / Organik çözücü toleranslı ve ısıya dayanıklı rekombinan E. coli lipaz üretiminin kinetiği ve grup fermentasyonu modellemesi

2015 ◽  
Vol 40 (4) ◽  
Author(s):  
Arbakariya Bin Ariff ◽  
Rubina Nelofer ◽  
Raja Nor Zaliha Raja Abdul Rahman ◽  
Mahiran Basri
Keyword(s):  
Cell Growth ◽  
Shake Flask ◽  
Lipase Production ◽  
Stirred Tank ◽  
Thermostable Lipase ◽  
Stirred Tank Bioreactor ◽  
Monod Equation ◽  
E Coli ◽  
Organic Solvent Tolerant ◽  
Solvent Tolerant

AbstractObjective: Kinetics of organic solvent tolerant and thermostable lipase production by recombinant E. coli in shake flask level and 2 L stirred tank bioreactor level was studied to observe the variations of important kinetic parameters at two different levels of bioprocess.Methods: Unstructured models based on Monod equation for growth and Luedeking-Piret equation for lipase production and glucose consumption were used to predict cell growth, lipase production and glucose utilization. The shake flask fermentation experiments were carried out at different initial glucose and yeast extract concentrations using recombinant bacterial strain E. coli BL21. Lipase production was also carried out using 2L stirred tank bioreactor for comparison.Results: In all cases, the data fitted well to the proposed models. The highest growth and lipase activity were obtained at 25 g/L glucose and 25 g/L yeast extract. Cell growth (6.42 g/L) and lipase production (65.32 IU/mL) in 2 L stirred tank bioreactor was comparable to those obtained in shake flask fermentations. The calculated value of growth associated constant (9.874 IU/g/h) was much higher than that of non-growth associated constant (0.022 IU/g/h) in bioreactor as well as in shake flasks. The values of maximum specific growth rate (μm) and glucose saturation constant (KS) for shake flask fermentations, calculated from Monod equation, were 0.476 h-1 and 5.237 g/L respectively.Conclusion: From the modelling exercise, it was concluded that the lipase production is dominantly growth associated process. The kinetic parameter values for fermentations in shake flask and 2L stirred tank bioreactor were comparable, indicating that the bioprocess could be transferred into larger scale.

Characterization and feasibility of a miniaturized stirred tank bioreactor to perform E. coli high cell density fed-batch fermentations

2011 ◽  
Vol 28 (1) ◽  
pp. 66-75 ◽  
Author(s):  
Shaukat Ali ◽  
Miguel Angel Perez-Pardo ◽  
Jean P. Aucamp ◽  
Alan Craig ◽  
Daniel G. Bracewell ◽  
...  
Keyword(s):  
Cell Density ◽  
High Cell Density ◽  
Stirred Tank ◽  
High Cell ◽  
Fed Batch ◽  
Stirred Tank Bioreactor ◽  
E Coli

scholarly journals Open-Source bioreactor controller for bacterial protein expression

2018 ◽  
Author(s):  
George Catalin Marinescu ◽  
Roua Gabriela Popescu
Keyword(s):  
Protein Expression ◽  
Open Source ◽  
Laboratory Experiments ◽  
Environmental Parameters ◽  
Cost Effective ◽  
Stirred Tank ◽  
Bacterial Protein ◽  
Process Data ◽  
Stirred Tank Bioreactor ◽  
E Coli

Growing microorganisms for laboratory experiments or industrial biotechnological process is an activity which involves the use of bioreactors. Although there are many commercially available equipment, most of them lack the flexibility of an open-source solution. This work proposes a cost effective Arduino based bioreactor controller for growing suspended microbial cells. To exemplify its functionality, this study provides the parts list and schematics necessary to make a functional laboratory scale bench top stirred tank bioreactor. Using the built prototype, an E. coli culture is grown maintaining the preset parameters, protein expression is induced and culture is harvested at preset culture density. Automatically recorded process data shows stable environmental parameters and reliable bacterial growing curve.

scholarly journals Open-Source bioreactor controller for bacterial protein expression

2018 ◽  
Author(s):  
George Catalin Marinescu ◽  
Roua Gabriela Popescu
Keyword(s):  
Protein Expression ◽  
Open Source ◽  
Laboratory Experiments ◽  
Environmental Parameters ◽  
Cost Effective ◽  
Stirred Tank ◽  
Bacterial Protein ◽  
Process Data ◽  
Stirred Tank Bioreactor ◽  
E Coli

Growing microorganisms for laboratory experiments or industrial biotechnological process is an activity which involves the use of bioreactors. Although there are many commercially available equipment, most of them lack the flexibility of an open-source solution. This work proposes a cost effective Arduino based bioreactor controller for growing suspended microbial cells. To exemplify its functionality, this study provides the parts list and schematics necessary to make a functional laboratory scale bench top stirred tank bioreactor. Using the built prototype, an E. coli culture is grown maintaining the preset parameters, protein expression is induced and culture is harvested at preset culture density. Automatically recorded process data shows stable environmental parameters and reliable bacterial growing curve.

Ribosome Structural Organization

1974 ◽  
Vol 32 ◽  
pp. 332-333
Author(s):  
James A. Lake
Keyword(s):  
Ribosomal Proteins ◽  
Structural Organization ◽  
Three Dimensional ◽  
Small Subunit ◽  
Structural Studies ◽  
X Ray Diffraction ◽  
Specific Antibodies ◽  
X Ray ◽  
E Coli ◽  
Complete Sequences

The understanding of ribosome structure has advanced considerably in the last several years. Biochemists have characterized the constituent proteins and rRNA's of ribosomes. Complete sequences have been determined for some ribosomal proteins and specific antibodies have been prepared against all E. coli small subunit proteins. In addition, a number of naturally occuring systems of three dimensional ribosome crystals which are suitable for structural studies have been observed in eukaryotes. Although the crystals are, in general, too small for X-ray diffraction, their size is ideal for electron microscopy.

Structural Role of rRNAs on the Ribosomal Subunits from E. Coli by Scanning Transmission Electron Microscopy

1981 ◽  
Vol 39 ◽  
pp. 424-425
Author(s):  
M. Boublik ◽  
N. Robakis ◽  
J.S. Wall
Keyword(s):  
Three Dimensional ◽  
Uranyl Acetate ◽  
Dimensional Structure ◽  
Electron Microscopic ◽  
Ribosomal Subunits ◽  
E Coli ◽  
Freeze Dried ◽  
16S Rna ◽  
Scanning Transmission ◽  
And Function

The three-dimensional structure and function of biological supramolecular complexes are, in general, determined and stabilized by conformation and interactions of their macromolecular components. In the case of ribosomes, it has been suggested that one of the functions of ribosomal RNAs is to act as a scaffold maintaining the shape of the ribosomal subunits. In order to investigate this question, we have conducted a comparative TEM and STEM study of the structure of the small 30S subunit of E. coli and its 16S RNA.The conventional electron microscopic imaging of nucleic acids is performed by spreading them in the presence of protein or detergent; the particles are contrasted by electron dense solution (uranyl acetate) or by shadowing with metal (tungsten). By using the STEM on freeze-dried specimens we have avoided the shearing forces of the spreading, and minimized both the collapse of rRNA due to air drying and the loss of resolution due to staining or shadowing. Figure 1, is a conventional (TEM) electron micrograph of 30S E. coli subunits contrasted with uranyl acetate.

Visualisation of E. coli ribosomal RNA in situ by electron spectroscopic imaging and image averaging

1992 ◽  
Vol 50 (1) ◽  
pp. 466-467
Author(s):  
Daniel Beniac ◽  
George Harauz
Keyword(s):  
Ribosomal Rna ◽  
Three Dimensional ◽  
Spectroscopic Imaging ◽  
Electron Spectroscopic Imaging ◽  
E Coli ◽  
Microscopical Technique ◽  
Quantitative Image ◽  
Dimensional Reconstruction ◽  
Image Averaging ◽  
Protein Components

The structures of E. coli ribosomes have been extensively probed by electron microscopy of negatively stained and frozen hydrated preparations. Coupled with quantitative image analysis and three dimensional reconstruction, such approaches are worthwhile in defining size, shape, and quaternary organisation. The important question of how the nucleic acid and protein components are arranged with respect to each other remains difficult to answer, however. A microscopical technique that has been proposed to answer this query is electron spectroscopic imaging (ESI), in which scattered electrons with energy losses characteristic of inner shell ionisations are used to form specific elemental maps. Here, we report the use of image sorting and averaging techniques to determine the extent to which a phosphorus map of isolated ribosomal subunits can define the ribosomal RNA (rRNA) distribution within them.

Polymorphic phase transition of a membrane protein - analysis of continuous diffuse electron diffraction intensity

1986 ◽  
Vol 44 ◽  
pp. 166-167
Author(s):  
Douglas L. Dorset ◽  
Andrew K. Massalski
Keyword(s):  
Molecular Sieve ◽  
Three Dimensional ◽  
Pore Geometry ◽  
Two Dimensional ◽  
Diffraction Intensity ◽  
Polymorphic Phase Transition ◽  
E Coli ◽  
Crystallographic Study ◽  
Hexagonal Form ◽  
Polymorphic Forms

Matrix porin, the ompF gene product of E. coli, has been the object of a electron crystallographic study of its pore geometry in an attempt to understand its function as a membrane molecular sieve. Three polymorphic forms have been found for two-dimensional crystals reconstituted in phospholipid, two hexagonal forms with different lipid content and an orthorhombic form coexisting with and similar to the hexagonal form found after lipid loss. In projection these have been shown to retain the same three-fold pore triplet geometry and analyses of three-dimensional data reveal that the small hexagonal and orthorhombic polymorphs have similar structure as well as unit cell spacings.

Three-Dimensional Reconstruction of Two Forms of the Chaperonin GRO EL

1990 ◽  
Vol 48 (1) ◽  
pp. 258-259
Author(s):  
J.L. Carrascosa ◽  
G. Abella ◽  
S. Marco ◽  
M. Muyal ◽  
J.M. Carazo
Keyword(s):  
Three Dimensional ◽  
The Other ◽  
Two Dimensional ◽  
Series Method ◽  
Three Dimensional Reconstruction ◽  
Structural Components ◽  
E Coli ◽  
Dimensional Reconstruction ◽  
Morphogenetic Factors ◽  
Tilt Series

Chaperonins are a class of proteins characterized by their role as morphogenetic factors. They trantsiently interact with the structural components of certain biological aggregates (viruses, enzymes etc), promoting their correct folding, assembly and, eventually transport. The groEL factor from E. coli is a conspicuous member of the chaperonins, as it promotes the assembly and morphogenesis of bacterial oligomers and/viral structures.We have studied groEL-like factors from two different bacteria:E. coli and B.subtilis. These factors share common morphological features , showing two different views: one is 6-fold, while the other shows 7 morphological units. There is also a correlation between the presence of a dominant 6-fold view and the fact of both bacteria been grown at low temperature (32°C), while the 7-fold is the main view at higher temperatures (42°C). As the two-dimensional projections of groEL were difficult to interprete, we studied their three-dimensional reconstruction by the random conical tilt series method from negatively stained particles.

scholarly journals Molecular Shape Descriptors. 2. Quantitative Structure-Activity Relationships Based Upon Three-Dimensional Molecular Shape Descriptor

1985 ◽  
Vol 40 (11) ◽  
pp. 1114-1120
Author(s):  
loan Motoc ◽  
Garland R. Marshall
Keyword(s):  
Enzyme Inhibitor ◽  
Three Dimensional ◽  
Shape Descriptor ◽  
Molecular Shape ◽  
Quantitative Structure Activity Relationship ◽  
Quantitative Structure ◽  
E Coli ◽  
Interactional Pattern ◽  
Structure Activity ◽  
Quantitative Structure Activity Relationships

A methodology to incorporate the three-dimensional molecular shape descriptor (3 D-MSD) into a quantitative structure-activity relationship is discussed in detail. The 3 D-MSD is calculated and correlated with Kiapp values for a set of 2,4-diamino-5-benzylpyrimidines which inhibit E. coli DHFR. The correlation (n = 22, r = 0.95, s = 0.214, F = 55.10) indicates that the polarization interaction dominates the enzyme-inhibitor interactional pattern.

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