A systematic concept in bioprocess analysis and design

A systematic concept in bioprocess analysis and design is presented according to an integrating strategy as basis for a biotechnological methodology. A comparison illustrates analogies and significant differences between chemical and biological processes. The study of the interactions between environments and organisms includes influences of physical transport phenomena and also enzyme and metabolic regulations. In both cases the macroscopic principle with a formalkinetic approach is recommended for quantification purposes. The determination of the characteristic-time-regime with characteristic rate constants makesit possible to simplify mathematical modeling using the concepts of the rate-determining-step and quasistationarity. Finally, guidelines are summarized for the use of unstructured and structured kinetic models.     

Four analogies between biological and cultural/linguistic evolution

The intricate phenomena of biology on the one hand, and language and culture on the other, have inspired many writers to draw analogies between these two evolutionary systems. These analogies can be divided into four principal types: species/language, organism/concept, genes/culture, and cell/person. Here, it is argued that the last analogy--between cells and persons--is the most profound in several respects, and, more importantly, can be used to generate a number of empirical predictions. In the first half of the paper, the four analogies are each evaluated after briefly describing criteria for a good predictive analogy. In the second half of the paper, the cell/person analogy and predictions deriving from it are explored in detail.     

Improvement of chemostat performance via nonlinear oscillations

A novel operation strategy employing self-generated oscillation to imrpove the performances of bioreactors is proposed and applied to a model system consisting of two continuous stirredtank bioreators (CSTBs) connected in series. It is demonstrated via computation that the performance of the system (in terms of timeaveraged cell concentration) can be greatly enhanced by adopting the proposed strategy. The process concept presented and the results obtained in this paper are expected to have significant implications beyond the bioprocessing industry.     

Integrated biofabrication for electro-addressed in-film bioprocessing

Many recent advances in bioprocessing have been enabled by developments in miniaturization and microfluidics. A continuing challenge, however, is integrating multiple unit operations that require distinct spatial boundaries, especially with included labile biological components. We have suggested "biofabrication" as a means for organizing cells and biomolecules in complex configurations while preserving function of individual components. Polysaccharide films of chitosan and alginate that are assembled on-chip by electrodeposition are "smart" configurable interfaces that mediate communication between the biological systems and microfabricated devices. Here, we demonstrate the scalable performance of a production address, where incubated cells secrete antibodies, and a capture address, where secreted antibody is retained with specificity and subsequently assayed. The antibody exchange from one electro-address to another exemplifies integrated in-film bioprocessing, facilitated by the integrated biofabrication techniques used. This in-film approach enables complex processes without need for microfluidics and valving. Finally, we have shown scalability by reducing electrode sizes to a 1 mm scale without compromising film biofabrication or bioprocessing performance. The in situ reversible deposition of viable cells, productivity characterization, and capture of secreted antibodies could find use in bioprocessing applications such as clonal selection, run-to-run monitoring, initial scale-up, and areas including drug screening and biopsy analysis.     

Particulate bioprocessing: A novel process strategy for biorefineries

A novel process strategy based on particulate bioprocessing has been developed for the production of value-added chemicals and biofuels. The process, which involves two main steps, fungal fermentation and discontinuous extraction, leads to the production of generic fermentation feedstocks from cereals. Partially pearled whole wheat grains were used as substrate for the growth of Aspergillus awamori in a packed bed bioreactor. Water was trickled through the bed of particles intermittently every 6 h to extract glucose and other nutrients and to maintain moisture and temperature levels. The feedstocks obtained through this system have been used for subsequent fermentations by Wautersia eutropha to produce the biodegradable plastic PHB (polyhydroxybutyrate) and by Saccharomyces cerevisiae for ethanol production. These preliminary results demonstrate the potential suitability of the novel concept of particulate bioprocessing in the development of biorefineries.     

Designing a blueprint for next-generation stem cell bioprocessing development

The creation of a blueprint for stem cell bioprocess development that it is easily readable and shareable among those involved in the construction of the bioprocess is a necessary step toward full-fledged bioprocess integration. The blueprint provides the culturing tools and methodologies, designed to highlight knowledge gaps within biological sciences and bioengineering. This review highlights a blueprint for stem cell bioprocessing development using a landscape architecture approach that can aid the development of culture technologies and tools that satisfy the demands for stem cell-derived products for use in clinical and industrial applications. This work is intended to provide insights to cell biologists, geneticists, bioengineers, and clinicians seeking knowledge outside of their field of expertise and fosters a leap from a reductionist approach to one, that is, globally integrated in stem cell bioprocessing.     

Advances in ethanol production from hardwood spent sulphite liquors

Hardwood spent sulphite liquors (HSSLs) are by-products from the pulping industry rich in pentoses, which are not yet fully exploited for bioprocessing, namely for the production of bioethanol. The sustainable fermentation of pentoses into bioethanol is a challenge to overcome. Besides sugars, HSSLs contains inhibitors that decrease the possibility of bioprocessing of these by-products. Nevertheless, recent studies have brought new insights in using HSSLs for bioethanol production. This paper reviews the results of relevant studies carried out with HSSLs towards bioprocessing to bioethanol. The composition of SSLs was compared and related with the wood origin stressing specificity of microbial inhibitors from HSSL and their anti-microbial effect. The different fermentative processes, the microorganisms used, and the strategies to improve yield and productivity used so far were also reviewed. This review allowed concluding that research is still needed in several areas, including optimization of detoxification processes, fermentation strategies and selection of suitable microbial strains in order to achieve the integration of the different steps needed for HSSLs bioconversion into ethanol thus contributing for sustainability of pulping mills within biorefinary concept.     

Industrial Biosystems Engineering and Biorefinery Systems

The concept of Industrial Biosystems Engineering (IBsE) was suggested as a new engineering branch to be developed for meeting the needs for science, technology and professionals by the upcoming bioeconomy. With emphasis on systems, IBsE builds upon the interfaces between systems biology, bioprocessing, and systems engineering. This paper discussed the background, the suggested definition, the theoretical framework and methodologies of this new discipline as well as its challenges and future development.     

Industrial Biosystems Engineering and Biorefinery Systems

The concept of Industrial Biosystems Engineering (IBsE) was suggested as a new engineering branch to be developed for meeting the needs for science, technology and professionals by the upcoming bioeconomy. With emphasis on systems, IBsE builds upon the interfaces between systems biology, bioprocessing, and systems engineering. This paper discussed the background, the suggested definition, the theoretical framework and methodologies of this new discipline as well as its challenges and future development     

Antimicrobial activity against select food-borne pathogens by phenolic antioxidants enriched in cranberry pomace by solid-state bioprocessing using the food grade fungus Rhizopus oligosporus

Listeria monocytogenes, Vibrio parahaemolyticus and Escherichia coli 0157:H7 are important food-borne pathogens. Control of these pathogens using synthetic antimicrobials such as currently approved antibiotics is challenging due to potential development of resistance. A profile of antimicrobials compared to a single compound could be potentially more effective. Cranberry pomace is a byproduct of the cranberry processing industry. Solid-state bioprocessing of cranberry pomace using the food grade fungus Rhizopus oligosporus improves phenolic and antioxidant profiles. We hypothesize that these phytochemicals mobilized during pomace bioprocessing could improve the antimicrobial functionality. The objective of this research was to use the food grade fungus R. oligosporus to release phenolic aglycones and relate its antioxidant functionality and diphenyl mobilization to antimicrobial activity against L. monocytogenes, V. parahaemolyticus and E. coli 0157:H7. Bioprocessing of pomace was done for 20 days with R. oligosporus. Total phenolics in water extracts were assayed using a Folin-Ciocalteu method. The antioxidant potential was measured using a β-carotene oxidation system (APF) and 1,1-diphenyl-2-picrylhydrazyl-radical (DPPH) system. Changes in phenolic profiles were analyzed using HPLC. Antimicrobial activities of the extracts during growth were tested using standard disk assays. Soluble phenolics, antioxidant activity and ellagic acid concentrations were enriched by bioprocessing and antimicrobial activity of the extracts against L. monocytogenes and V. parahaemolyticus correlated with highest soluble phenolics and APF in the same extracts. For E. coli 0157:H7 inhibition correlated with the extracts corresponding to highest DPPH and ellagic acid concentration. The bioprocessing-based antimicrobial activity depended on different phenolic functional properties of the extracts. Sensitivity towards soluble phenolics reflected in DPPH activity suggested inhibition by the disruption of the membrane by hyperacidification. Whereas, sensitivity to APF and ellagic acid suggests potential antimicrobial activity by membrane-transport disruption. The variation in sensitivity of pathogens has implications for designing new food grade antimicrobials. This bioprocessing strategy can be an innovative approach to produce broad spectrum antimicrobials against important food-borne pathogens.     

Continuous bioprocessing: The real thing this time?

The Annual bioProcessUK Conference has acted as the key networking event for bioprocess scientists and engineers in the UK for the past 10 years. The following article is a report from the sessions that focused on continuous bioprocessing during the 10^th Annual bioProcessUK Conference (London, December 2013). These sessions were organized by the ‘EPSRC Centre for Innovative Manufacturing in Emergent Macromolecular Therapies’ hosted at University College London. A plenary lecture and workshop provided a forum for participants to debate topical issues in roundtable discussions with industry and academic experts from institutions such as Genzyme, Janssen, Novo Nordisk, Pfizer, Merck, GE Healthcare and University College London. The aim of these particular sessions was to understand better the challenges and opportunities for continuous bioprocessing in the bioprocessing sector.     

Continuous bioprocessing: The real thing this time?: 10th Annual bioProcessUK Conference,December 3–4, 2013, London,UK

The Annual bioProcessUK Conference has acted as the key networking event for bioprocess scientists and engineers in the UK for the past 10 years. The following article is a report from the sessions that focused on continuous bioprocessing during the 10^th Annual bioProcessUK Conference (London, December 2013). These sessions were organized by the ‘EPSRC Centre for Innovative Manufacturing in Emergent Macromolecular Therapies’ hosted at University College London. A plenary lecture and workshop provided a forum for participants to debate topical issues in roundtable discussions with industry and academic experts from institutions such as Genzyme, Janssen, Novo Nordisk, Pfizer, Merck, GE Healthcare and University College London. The aim of these particular sessions was to understand better the challenges and opportunities for continuous bioprocessing in the bioprocessing sector.     

Analogies in science and science teaching

Analogies are often used in science, but students may not appreciate their significance, and so the analogies can be misunderstood or discounted. For this reason, educationalists often express concern about the use of analogies in teaching. Given the important place of analogies in the discourse of science, it is necessary that students are explicitly shown how they work, perhaps based on the structure-mapping theory we outline here. When using an analogy, the teacher should very clearly specify both its components and its limitations. Great care is required in developing an analogy to ensure that it is understood as intended and that misconceptions are minimized. This approach models the behavior of a scientist, which helps to develop student understanding of the practice of science.     

Modeling of esterase production from Saccharomyces cerevisiae

A suitable simple model tested by experiments is required to address complex biological reactions like esterase synthesis by Saccharomyces cerevisiae. Such an approach might be the answer to a proper bioprocessing strategy. In this regard, a logistic model for esterase production from Saccharomyces cerevisiae has been developed, which predicts well the cell mass, the carbon source (glucose) consumption, and the esterase activity. The accuracy of the model has been statistically examined by using the Student's t-test. The parameter sensitivity analysis showed that all five parameters (microm, Ks, Xm, Yx/s, and Yp/x) have significant influence on the predicted values of esterase activity.     

Fluid network response characteristics under pulsating flow conditions

The strong analogies between electrical and fluid system can be used to effect in modeling behaviour under pulsating flow conditions. This paper discusses the model of a simple pipe network experiencing pulsating flow as a result of valve movement. Experimental results are presented, indicating that care needs to be taken in modeling the valve behaviour as analogous to thermionic valve.

One of the major problems in modeling fluid networks of this type is the lack of information regarding the characteristics of active components such as the valve. Developments in the field of Electro-magnetic and Ultrasonic flow measurement are helping to improve this situation.     

New disposable tubes for rapid and precise biomass assessment for suspension cultures of mammalian cells

We present a new approach for biomass assessment in cell culture using a disposable microcentrifuge tube. The specially designed tube is fitted with an upper chamber for sample loading and a lower 5 microL capillary for cell collection during centrifugation. The resulting packed cell volume (PCV) can be quantitatively expressed as the percentage of the total volume of the sample. The present study focused on the validation of the method with mammalian cell lines that are widely used in bioprocessing. Using several examples, the PCV method was shown to be more precise, rapid, and reproducible than manual cell counting.     

Visual representation of DNA sequences for exon detection using non-parametric spectral estimation techniques

This paper presents a new approach for modeling of DNA sequences for the purpose of exon detection. The proposed model adopts the sum-of-sinusoids concept for the representation of DNA sequences. The objective of the modeling process is to represent the DNA sequence with few coefficients. The modeling process can be performed on the DNA signal as a whole or on a segment-by-segment basis. The created models can be used instead of the original sequences in a further spectral estimation process for exon detection. The accuracy of modeling is evaluated evaluated by using the Root Mean Square Error (RMSE) and the R-square metrics. In addition, non-parametric spectral estimation methods are used for estimating the spectral of both original and modeled DNA sequences. The results of exon detection based on original and modeled DNA sequences coincide to a great extent, which ensures the success of the proposed sum-of-sinusoids method for modeling of DNA sequences.     

From ‘ecologist’ to ‘conceptual ecologist’: the utility of the conceptual ecology analogy for teachers of biology

This paper advocates the application of established teaching models to the professional development of biology teachers. This is achieved by using the analogy of conceptual ecologies, made explicit through concept mapping. The approach is designed to support teachers' developing understanding of pupils' conceptual change by using familiar terminology and biological analogies. Monitoring of students' understanding at an ecosystemic level may also help distinguish between instances of conceptual change and contextual switching (described here with reference to photosynthesis).     

Information Sets and Excess Zeros in Random Effects Modeling of Longitudinal Data

Marginal regression via generalized estimating equations is widely used in biostatistics to model longitudinal data from subjects whose outcomes and covariates are observed at several time points. In this paper we consider two issues that have been raised in the literature concerning the marginal regression approach. The first is that even though the past history may be predictive of outcome, the marginal approach does not use this history. Although marginal regression has the flexibility of allowing between-subject variations in the observation times, it may lose substantial prediction power in comparison with the transitional modeling approach that relates the responses to the covariate and outcome histories. We address this issue by using the concept of “information sets” for prediction to generalize the “partly conditional mean” approach of Pepe and Couper (J. Am. Stat. Assoc. 92:991–998, 1997). This modeling approach strikes a balance between the flexibility of the marginal approach and the predictive power of transitional modeling. Another issue is the problem of excess zeros in the outcomes over what the underlying model for marginal regression implies. We show how our predictive modeling approach based on information sets can be readily modified to handle the excess zeros in the longitudinal time series. By synthesizing the marginal, transitional, and mixed effects modeling approaches in a predictive framework, we also discuss how their respective advantages can be retained while their limitations can be circumvented for modeling longitudinal data.     

Current state of the art in continuous bioprocessing

There is an upsurge of interest in continuous bioprocessing, but currently continuous downstream bioprocessing has not been implemented to generate clinical material. This review focusses on the current state of the art of continuous downstream processing, highlighting the key advantages over traditional batch manufacturing. This allows the identification of scenarios where continuous downstream processing may be critical for commercial manufacturing success.