scholarly journals Strategies for Enhancing Product Yield: Design of Experiments (DOE) for Escherichia coli Cultivation

2021 ◽  
Author(s):  
Puneet Kumar Gupta ◽  
Jyotheeswara Reddy Edula
Keyword(s):  
Design Of Experiments ◽  
Process Development ◽  
Model Organism ◽  
Cost Effective ◽  
Product Yield ◽  
E Coli ◽  
Effective Manner ◽  
Production Temperature ◽  
Shake Flasks ◽  
Biopharmaceutical Production

E. coli is considered one of the best model organism for biopharmaceutical production by fermentation. Its utility in process development is employed to develop various vaccines, metabolites, biofuels, antibiotics and synthetic molecules in large amounts based on the amount of yield in shake flasks, bioreactors utilised by batch, fed-batch and continuous mode. Production of the desired molecule is facilitated in the bioreactor by employing strategies to increase biomass and optimised yield. The fermentation is a controlled process utilising media buffers, micronutrients and macronutrients, which is not available in a shake flask. To maximise the production temperature, dissolved oxygen (aerobic), dissolved nitrogen (anaerobic), inducer concentration, feed or supplementation of nutrients is the key to achieving exponential growth rate and biomass. Design of experiments (DOE) is critical for attaining maximum gain, in cost-effective manner. DOE comprises of several strategies likewise Plakett-Burman., Box–Behnken, Artificial Neural Network, combination of these strategies leads to reduction of cost of production by 2–8 times depending on molecules to be produced. Further minimising downstream process for quickly isolation, purification and enrichment of the final product.

Design of experiments – overcome hindrances and bad practices

2019 ◽  
Vol 31 (5) ◽  
pp. 772-789
Author(s):  
Nuno Costa
Keyword(s):  
Design Of Experiments ◽  
Business Performance ◽  
Cost Effective ◽  
Content Type ◽  
Designed Experiments ◽  
Effective Manner ◽  
Technical Competencies ◽  
Design And Manufacturing ◽  
Practical Implications ◽  
Durability Performance

Purpose The purpose of this paper is to address misconceptions about the design of experiments (DoE) usefulness, avoid bad practices and foster processes’ efficiency and products’ quality in a timely and cost-effective manner with this tool. Design/methodology/approach To revisit and discuss the hindrances to DoE usage as well as bad practices in using this tool supported on the selective literature from Web of Science and Scopus indexed journals. Findings A set of recommendations and guidelines to mitigate DoE hindrances and avoid common errors or wrong decisions at the planning, running and data analysis phases of DoE are provided. Research limitations/implications Errors or wrong decisions in planning, running and analyzing data from statistically designed experiments are always possible so the expected results from DoE usage are not always 100 percent guaranteed. Practical implications Novice and intermediate DoE users have another perspective for developing and improving their “test and learn” capability and be successful with DoE. To appropriately plan and run statistically designed experiments not only save the user of DoE from incorrect decisions and depreciation of their technical competencies as they can optimize processes’ efficiency and products’ quality (reliability, durability, performance, robustness, etc.) in a structured, faster and cheaper way at the design and manufacturing stages. Social implications DoE usefulness will be increasingly recognized in industry and academy and, as consequence, better products can be made available for consumers, business performance can improve, and the link between industry and academy can be strengthened. Originality/value A supplemental perspective on how to succeed with DoE and foster its usage among managers, engineers and other technical staff is presented.

scholarly journals BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species

2014 ◽  
Vol 11 (2) ◽  
pp. 106-119 ◽  
Author(s):  
Goksel Misirli ◽  
Jennifer Hallinan ◽  
Richard Röttger ◽  
Jan Baumbach ◽  
Anil Wipat
Keyword(s):  
Regulatory Networks ◽  
Sequence Data ◽  
Model Organism ◽  
Cost Effective ◽  
Bacillus Species ◽  
Biological Behaviour ◽  
Promoter Sequences ◽  
Effective Manner ◽  
Close Relatives ◽  
Analysis Platform

Summary As high-throughput technologies become cheaper and easier to use, raw sequence data and corresponding annotations for many organisms are becoming available. However, sequence data alone is not sufficient to explain the biological behaviour of organisms, which arises largely from complex molecular interactions. There is a need to develop new platform technologies that can be applied to the investigation of whole-genome datasets in an efficient and cost-effective manner. One such approach is the transfer of existing knowledge from well-studied organisms to closely-related organisms. In this paper, we describe a system, BacillusRegNet, for the use of a model organism, Bacillus subtilis, to infer genome-wide regulatory networks in less well-studied close relatives. The putative transcription factors, their binding sequences and predicted promoter sequences along with annotations are available from the associated BacillusRegNet website (http://bacillus.ncl.ac.uk).

scholarly journals Use of Miniaturized Protein Arrays for Escherichia coli O Serotyping

2006 ◽  
Vol 13 (5) ◽  
pp. 561-567 ◽  
Author(s):  
Muna F. Anjum ◽  
James D. Tucker ◽  
Katherine A. Sprigings ◽  
Martin J. Woodward ◽  
Ralf Ehricht
Keyword(s):  
Escherichia Coli ◽  
Cost Effective ◽  
Protein Arrays ◽  
Microarray Chip ◽  
E Coli ◽  
Effective Manner ◽  
Serological Typing ◽  
Independent Test ◽  
Increased Sensitivity ◽  
O Antigens

ABSTRACT Serological typing of Escherichia coli O antigens is a well-established method used for differentiation and identification of O serotypes commonly associated with disease. In this feasibility study, we have developed a novel somatic antibody-based miniaturized microarray chip, using 17 antisera, which can be used to detect bound whole-cell E. coli antigen with its corresponding immobilized antibody, to assess the feasibility of this approach. The chip was tested using the related 17 control strains, and the O types found by the microarray chip showed 100% correlation with the O types found by conventional typing. A blind trial was performed in which 100 E. coli isolates that had been O serotyped previously by the conventional assay were tested by the array approach. Overall, the O serotypes of 88% of isolates were correctly identified by the microarray method. For several isolates, ambiguity of O-type designation by microarray arose due to increased sensitivity of this method, allowing signal intensities of cross-reactions to be quantified. Investigation of discrepancies between conventional and microarray O serotyping indicated that some isolates upon storage had become untypeable and, therefore, gave poor signal intensity when tested by the microarray or retested by conventional means. For all 20 serotype O26 and O157 isolates, the apparent discrepancy in O serotyping was analyzed further by a third independent test, which confirmed the microarray results. Therefore, the use of miniaturized protein arrays increases the speed and efficiency of O serotyping in a cost-effective manner, and these preliminary findings suggest the microarray approach may have a higher accuracy than those of traditional O-serotyping methods.

Strategic planning in grassland farming: Principles andapplications

1997 ◽  
pp. 191-197
Author(s):  
W.J. Parker ◽  
N.M. Shadbolt ◽  
D.I. Gray
Keyword(s):  
Strategic Planning ◽  
Performance Indicators ◽  
Cost Effective ◽  
Key Performance Indicators ◽  
Strategic Plans ◽  
Effective Manner ◽  
Farm Business ◽  
Pastoral Farming ◽  
Financial Environment

Three levels of planning can be distinguished in grassland farming: strategic, tactical and operational. The purpose of strategic planning is to achieve a sustainable long-term fit of the farm business with its physical, social and financial environment. In pastoral farming, this essentially means developing plans that maximise and best match pasture growth with animal demand, while generating sufficient income to maintain or enhance farm resources and improvements, and attain personal and financial goals. Strategic plans relate to the whole farm business and are focused on the means to achieve future needs. They should be routinely (at least annually) reviewed and monitored for effectiveness through key performance indicators (e.g., Economic Farm Surplus) that enable progress toward goals to be measured in a timely and cost-effective manner. Failure to link strategy with control is likely to result in unfulfilled plans. Keywords: management, performance

Pollution, Toxicity and Carcinogenicity of Organic Dyes and their Catalytic Bio-Remediation

2019 ◽  
Vol 25 (34) ◽  
pp. 3645-3663 ◽  
Author(s):  
Muhammad Ismail ◽  
Kalsoom Akhtar ◽  
M.I. Khan ◽  
Tahseen Kamal ◽  
Murad A. Khan ◽  
...  
Keyword(s):  
Water Pollution ◽  
Textile Industry ◽  
Pathogenic Bacteria ◽  
Diarrheal Disease ◽  
Organic Dyes ◽  
Chemical Reduction ◽  
Cost Effective ◽  
Agricultural Runoff ◽  
E Coli ◽  
Sanitation Services

: Water pollution due to waste effluents of the textile industry is seriously causing various health problems in humans. Water pollution with pathogenic bacteria, especially Escherichia coli (E. coli) and other microbes is due to the mixing of fecal material with drinking water, industrial and domestic sewage, pasture and agricultural runoff. Among the chemical pollutants, organic dyes due to toxic nature, are one of the major contaminants of industrial wastewater. Adequate sanitation services and drinking quality water would eliminate 200 million cases of diarrhea, which results in 2.1 million less deaths caused by diarrheal disease due to E. coli each year. Nanotechnology is an excellent platform as compared to conventional treatment methods of water treatment and remediation from microorganisms and organic dyes. In the current study, toxicity and carcinogenicity of the organic dyes have been studied as well as the remediation/inactivation of dyes and microorganism has been discussed. Remediation by biological, physical and chemical methods has been reviewed critically. A physical process like adsorption is cost-effective, but can’t degrade dyes. Biological methods were considered to be ecofriendly and cost-effective. Microbiological degradation of dyes is cost-effective, eco-friendly and alternative to the chemical reduction. Besides, certain enzymes especially horseradish peroxidase are used as versatile catalysts in a number of industrial processes. Moreover, this document has been prepared by gathering recent research works related to the dyes and microbial pollution elimination from water sources by using heterogeneous photocatalysts, metal nanoparticles catalysts, metal oxides and enzymes.

Quality Improvement of the DNA extracted by boiling method in Gram negative bacteria

2017 ◽  
Vol 6 (04) ◽  
pp. 5347 ◽  
Author(s):  
Omar B. Ahmed* ◽  
Anas S. Dablool
Keyword(s):  
Dna Extraction ◽  
Control Method ◽  
Extraction Procedure ◽  
Cost Effective ◽  
High Yield ◽  
Gram Negative Bacteria ◽  
Bacterial Dna ◽  
Gram Negative ◽  
E Coli

Several methods of Deoxyribonucleic acid (DNA) extraction have been applied to extract bacterial DNA. The amount and the quality of the DNA obtained for each one of those methods are variable. The study aimed to evaluate bacterial DNA extraction using conventional boiling method followed by alcohol precipitation. DNA extraction from Gram negative bacilli was extracted and precipitated using boiling method with further precipitation by ethanol. The extraction procedure performed using the boiling method resulted in high DNA yields for both E. coli and K. pneumoniae bacteria in (199.7 and 285.7μg/ml, respectively) which was close to control method (229.3 and 440.3μg/ml). It was concluded that after alcohol precipitation boiling procedure was easy, cost-effective, and applicable for high-yield quality of DNA in Gram-negative bacteria.

scholarly journals Software-guided microscale flow calorimeter for efficient acquisition of thermokinetic data

2021 ◽  
Author(s):  
Timothy Aljoscha Frede ◽  
Marlene Dietz ◽  
Norbert Kockmann
Keyword(s):  
Design Of Experiments ◽  
Process Development ◽  
Reaction Conditions ◽  
Experimental Conditions ◽  
Flow Calorimeter ◽  
Microscale Flow ◽  
Increased Sensitivity ◽  
Important Time ◽  
Optimal Reaction

AbstractFast chemical process development is inevitably linked to an optimized determination of thermokinetic data of chemical reactions. A miniaturized flow calorimeter enables increased sensitivity when examining small amounts of reactants in a short time compared to traditional batch equipment. Therefore, a methodology to determine optimal reaction conditions for calorimetric measurement experiments was developed and is presented in this contribution. Within the methodology, short-cut calculations are supplemented by computational fluid dynamics (CFD) simulations for a better representation of the hydrodynamics within the microreactor. This approach leads to the effective design of experiments. Unfavourable experimental conditions for kinetics experiments are determined in advance and therefore, need not to be considered during design of experiments. The methodology is tested for an instantaneous acid-base reaction. Good agreement of simulations was obtained with experimental data. Thus, the prediction of the hydrodynamics is enabled and the first steps towards a digital twin of the calorimeter are performed. The flow rates proposed by the methodology are tested for the determination of reaction enthalpy and showed that reasonable experimental settings resulted. Graphical abstract A methodology is suggested to evaluate optimal reaction conditions for efficientacquisition of kinetic data. The experimental design space is limited by thestepwise determination of important time scales based on specified input data.

scholarly journals Novel Regeneration Approach for Creating Reusable FO-SPR Probes with NTA Surface Chemistry

Nanomaterials ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 186
Author(s):  
Jia-Huan Qu ◽  
Karen Leirs ◽  
Remei Escudero ◽  
Žiga Strmšek ◽  
Roman Jerala ◽  
...  
Keyword(s):  
Surface Chemistry ◽  
Fluorescent Protein ◽  
Cost Effective ◽  
Nitrilotriacetic Acid ◽  
Antibody Fragments ◽  
Rapid Screening ◽  
Red Fluorescent Protein ◽  
Effective Manner ◽  
Surface Regeneration ◽  
Sensitivity Specificity

To date, surface plasmon resonance (SPR) biosensors have been exploited in numerous different contexts while continuously pushing boundaries in terms of improved sensitivity, specificity, portability and reusability. The latter has attracted attention as a viable alternative to disposable biosensors, also offering prospects for rapid screening of biomolecules or biomolecular interactions. In this context here, we developed an approach to successfully regenerate a fiber-optic (FO)-SPR surface when utilizing cobalt (II)-nitrilotriacetic acid (NTA) surface chemistry. To achieve this, we tested multiple regeneration conditions that can disrupt the NTA chelate on a surface fully saturated with His6-tagged antibody fragments (scFv-33H1F7) over ten regeneration cycles. The best surface regeneration was obtained when combining 100 mM EDTA, 500 mM imidazole and 0.5% SDS at pH 8.0 for 1 min with shaking at 150 rpm followed by washing with 0.5 M NaOH for 3 min. The true versatility of the established approach was proven by regenerating the NTA surface for ten cycles with three other model system bioreceptors, different in their size and structure: His6-tagged SARS-CoV-2 spike fragment (receptor binding domain, RBD), a red fluorescent protein (RFP) and protein origami carrying 4 RFPs (Tet12SN-RRRR). Enabling the removal of His6-tagged bioreceptors from NTA surfaces in a fast and cost-effective manner can have broad applications, spanning from the development of biosensors and various biopharmaceutical analyses to the synthesis of novel biomaterials.

scholarly journals High-throughput microbioreactor provides a capable tool for early stage bioprocess development

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mathias Fink ◽  
Monika Cserjan-Puschmann ◽  
Daniela Reinisch ◽  
Gerald Striedner
Keyword(s):  
High Throughput ◽  
Process Development ◽  
Early Stage ◽  
Explanatory Power ◽  
Batch Mode ◽  
E Coli ◽  
Speed Up ◽  
Bioreactor System ◽  
Cell Densities ◽  
Microbial Systems

AbstractTremendous advancements in cell and protein engineering methodologies and bioinformatics have led to a vast increase in bacterial production clones and recombinant protein variants to be screened and evaluated. Consequently, an urgent need exists for efficient high-throughput (HTP) screening approaches to improve the efficiency in early process development as a basis to speed-up all subsequent steps in the course of process design and engineering. In this study, we selected the BioLector micro-bioreactor (µ-bioreactor) system as an HTP cultivation platform to screen E. coli expression clones producing representative protein candidates for biopharmaceutical applications. We evaluated the extent to which generated clones and condition screening results were transferable and comparable to results from fully controlled bioreactor systems operated in fed-batch mode at moderate or high cell densities. Direct comparison of 22 different production clones showed great transferability. We observed the same growth and expression characteristics, and identical clone rankings except one host-Fab-leader combination. This outcome demonstrates the explanatory power of HTP µ-bioreactor data and the suitability of this platform as a screening tool in upstream development of microbial systems. Fast, reliable, and transferable screening data significantly reduce experiments in fully controlled bioreactor systems and accelerate process development at lower cost.

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