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Bioprocessing

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https://www.readbyqxmd.com/read/29225230/in-situ-measurement-of-the-ph-dependent-transmission-infrared-spectra-of-aqueous-lactic-acid-solutions
#1
Takuji Ube, Yasuko Yoneyama, Takashi Ishiguro
The transmission infrared absorption spectra of an aqueous lactic acid solution was measured over a pH range of 2.66 - 1.59 using a cell with an optical path length of 12 μm. Absorption peaks were then identified by density functional theory (DFT) calculations. The observed pH-dependent changes in the absorbance spectra were consistent with the properties of the assigned functional groups. We therefore believe that the present method can be applied to the contactless and non-invasive quantitative evaluation of pH values in aqueous systems, such as bioprocesses and bioimaging...
2017: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
https://www.readbyqxmd.com/read/29224081/electrochemical-applications-in-metal-bioleaching
#2
Christoph Kurt Tanne, Axel Schippers
Biohydrometallurgy comprises the recovery of metals by biologically catalyzed metal dissolution from solids in an aqueous solution. The application of this kind of bioprocessing is described as "biomining," referring to either bioleaching or biooxidation of sulfide metal ores. Acidophilic iron- and sulfur-oxidizing microorganisms are the key to successful biomining. However, minerals such as primary copper sulfides are recalcitrant to dissolution, which is probably due to their semiconductivity or passivation effects, resulting in low reaction rates...
December 10, 2017: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/29223022/next-generation-industrial-biotechnology-based-on-extremophilic-bacteria
#3
REVIEW
Guo-Qiang Chen, Xiao-Ran Jiang
Industrial biotechnology aims to produce bulk chemicals including polymeric materials and biofuels based on bioprocessing sustainable agriculture products such as starch, fatty acids and/or cellulose. However, traditional bioprocesses require bioreactors made of stainless steel, complicated sterilization, difficult and expensive separation procedures as well as well-trained engineers that are able to conduct bioprocessing under sterile conditions, reducing the competitiveness of the bio-products. Amid the continuous low petroleum price, next generation industrial biotechnology (NGIB) allows bioprocessing to be conducted under unsterile (open) conditions using ceramic, cement or plastic bioreactors in a continuous way, it should be an energy, water and substrate saving technology with convenient operation procedure...
December 6, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29223005/the-emerging-role-of-systems-biology-for-engineering-protein-production-in-cho-cells
#4
REVIEW
Chih-Chung Kuo, Austin Wt Chiang, Isaac Shamie, Mojtaba Samoudi, Jahir M Gutierrez, Nathan E Lewis
To meet the ever-growing demand for effective, safe, and affordable protein therapeutics, decades of intense efforts have aimed to maximize the quantity and quality of recombinant proteins produced in CHO cells. Bioprocessing innovations and cell engineering efforts have improved product titer; however, uncharacterized cellular processes and gene regulatory mechanisms still hinder cell growth, specific productivity, and protein quality. Herein, we summarize recent advances in systems biology and data-driven approaches aiming to unravel how molecular pathways, cellular processes, and extrinsic factors (e...
December 6, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29222762/dynamic-flux-balance-analysis-using-dfbalab
#5
Jose Alberto Gomez, Paul I Barton
Bioprocesses are of critical importance in several industries such as the food and pharmaceutical industries. Despite their importance and widespread application, bioprocess models remain rather simplistic and based on unstructured models. These simple models have limitations, making it very difficult to model complex bioprocesses. With dynamic flux balance analysis (DFBA) more comprehensive bioprocess models can be obtained. DFBA simulations are difficult to carry out because they result in dynamic systems with linear programs embedded...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29217872/an-integrated-bioprocess-to-recover-bovine-milk-oligosaccharides-from-colostrum-whey-permeate
#6
Juliana M L N de Moura Bell, Joshua L Cohen, Leticia F M C de Aquino, Hyeyoung Lee, Vitor L de Melo Silva, Yan Liu, Paola Domizio, Daniela Barile
A major challenge in isolating oligosaccharides from dairy streams is to enrich oligosaccharides while simultaneously reducing the content of simple sugars (mono- and disaccharides) that do not possess the desired prebiotic functions. An integrated approach based on optimized conditions that favor maximum lactose hydrolysis, monosaccharide fermentation and oligosaccharides recovery by nanofiltration was developed. Upon complete lactose hydrolysis and fermentation of the monosaccharides by yeast, nanofiltration of fermented whey permeate from colostrum enabled the recovery of 95% of the oligosaccharides at high purity...
January 2018: Journal of Food Engineering
https://www.readbyqxmd.com/read/29216497/engineering-the-bioconversion-of-methane-and-methanol-to-fuels-and-chemicals-in-native-and-synthetic-methylotrophs
#7
REVIEW
R Kyle Bennett, Lisa M Steinberg, Wilfred Chen, Eleftherios T Papoutsakis
Methylotrophy describes the ability of organisms to utilize reduced one-carbon compounds, notably methane and methanol, as growth and energy sources. Abundant natural gas supplies, composed primarily of methane, have prompted interest in using these compounds, which are more reduced than sugars, as substrates to improve product titers and yields of bioprocesses. Engineering native methylotophs or developing synthetic methylotrophs are emerging fields to convert methane and methanol into fuels and chemicals under aerobic and anaerobic conditions...
December 4, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29215210/a-comparative-transcriptomics-workflow-for-analyzing-microarray-data-from-cho-cell-cultures
#8
Chun Chen, Huong Le, Brian Follstad, Chetan T Goudar
Microarray-based comparative transcriptomics analysis is a powerful tool to understand therapeutic protein producing mammalian cell lines at the gene expression level. However, an integrated analysis workflow specifically designed for end-to-end analysis of microarray data for CHO cells, the most prevalent host for commercial recombinant protein production, is lacking. To address this gap, we have developed an automated data analysis workflow in R that leverages public domain analysis modules to analyze microarray based gene expression data...
December 7, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/29213318/targeted-redox-and-energy-cofactor-metabolomics-in-clostridium-thermocellum-and-thermoanaerobacterium-saccharolyticum
#9
Kyle Sander, Keiji G Asano, Deepak Bhandari, Gary J Van Berkel, Steven D Brown, Brian Davison, Timothy J Tschaplinski
Background: Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are prominent candidate biocatalysts that, together, can enable the direct biotic conversion of lignocellulosic biomass to ethanol. The imbalance and suboptimal turnover rates of redox cofactors are currently hindering engineering efforts to achieve higher bioproductivity in both organisms. Measuring relevant intracellular cofactor concentrations will help understand redox state of these cofactors and help identify a strategy to overcome these limitations; however, metabolomic determinations of these labile metabolites have historically proved challenging...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29213312/adding-tetrahydrofuran-to-dilute-acid-pretreatment-provides-new-insights-into-substrate-changes-that-greatly-enhance-biomass-deconstruction-by-clostridium-thermocellum-and-fungal-enzymes
#10
Vanessa A Thomas, Bryon S Donohoe, Mi Li, Yunqiao Pu, Arthur J Ragauskas, Rajeev Kumar, Thanh Yen Nguyen, Charles M Cai, Charles E Wyman
Background: Consolidated bioprocessing (CBP) by anaerobes, such as Clostridium thermocellum, which combine enzyme production, hydrolysis, and fermentation are promising alternatives to historical economic challenges of using fungal enzymes for biological conversion of lignocellulosic biomass. However, limited research has integrated CBP with real pretreated biomass, and understanding how pretreatment impacts subsequent deconstruction by CBP vs. fungal enzymes can provide valuable insights into CBP and suggest other novel biomass deconstruction strategies...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29213311/expression-of-adha-from-different-organisms-in-clostridium-thermocellum
#11
Tianyong Zheng, Jingxuan Cui, Hye Ri Bae, Lee R Lynd, Daniel G Olson
Background: Clostridium thermocellum is a cellulolytic anaerobic thermophile that is a promising candidate for consolidated bioprocessing of lignocellulosic biomass into biofuels such as ethanol. It was previously shown that expressing Thermoanaerobacterium saccharolyticum adhA in C. thermocellum increases ethanol yield.In this study, we investigated expression of adhA genes from different organisms in Clostridium thermocellum. Methods: Based on sequence identity to T...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29213307/the-effect-of-switchgrass-loadings-on-feedstock-solubilization-and-biofuel-production-by-clostridium-thermocellum
#12
Tobin J Verbeke, Gabriela M Garcia, James G Elkins
Background: Efficient deconstruction and bioconversion of solids at high mass loadings is necessary to produce industrially relevant titers of biofuels from lignocellulosic biomass. To date, only a few studies have investigated the effect of solids loadings on microorganisms of interest for consolidated bioprocessing. Here, the effects that various switchgrass loadings have on Clostridium thermocellum solubilization and bioconversion are investigated. Results: Clostridium thermocellum was grown for 10 days on 10, 25, or 50 g/L switchgrass or Avicel at equivalent glucan loadings...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29213303/climbing-the-mountain-experimental-design-for-the-efficient-optimization-of-stem-cell-bioprocessing
#13
REVIEW
Derek Toms, Rob Deardon, Mark Ungrin
"To consult the statistician after an experiment is finished is often merely to ask him to conduct a post mortem examination. He can perhaps say what the experiment died of." - R.A. Fisher While this idea is relevant across research scales, its importance becomes critical when dealing with the inherently large, complex and expensive process of preparing material for cell-based therapies (CBTs). Effective and economically viable CBTs will depend on the establishment of optimized protocols for the production of the necessary cell types...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/29208557/demonstration-of-bioprocess-factors-optimization-for-enhanced-mono-rhamnolipid-production-by-a-marine-pseudomonas-guguanensis
#14
RamyaDevi K C, Lakshmi Sundaram R, Asha D, Sivamurugan V, Vidya Vasudevan, Mary Elizabeth Gnanambal Krishnan
We identified that Pseudomonas guguanensis produced macromolecular mono-rhamnolipid (Mol. Wt 1264.52Da) upon sensing n-hexadecane/diesel/kerosene from its surroundings. Permutation experiments were done to improve the laboratory-scale mono-rhamnolipid production (ie, a three-fold increase) using RSM validation. Consequently, maximal mono-rhamnolipids production [40-50mg/L] and emulsification abilities [65-70%] were encountered on day 8 using vegetable oil, peptone+yeast extract. EI24 values of the rhamnolipids were found to be 78±1...
December 2, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29206899/mosaic-a-chemical-genetic-interaction-data-repository-and-web-resource-for-exploring-chemical-modes-of-action
#15
Justin Nelson, Scott W Simpkins, Hamid Safizadeh, Sheena C Li, Jeff S Piotrowski, Hiroyuki Hirano, Yoko Yashiroda, Hiroyuki Osada, Minoru Yoshida, Charles Boone, Chad L Myers
Summary: Chemical-genomic approaches that map interactions between small molecules and genetic perturbations offer a promising strategy for functional annotation of uncharacterized bioactive compounds. We recently developed a new high-throughput platform for mapping chemical-genetic (CG) interactions in yeast that can be scaled to screen large compound collections, and we applied this system to generate CG interaction profiles for more than 13,000 compounds. When integrated with the existing global yeast genetic interaction network, CG interaction profiles can enable mode-of-action prediction for previously uncharacterized compounds as well as discover unexpected secondary effects for known drugs...
November 30, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29205280/maximizing-neotissue-growth-kinetics-in-a-perfusion-bioreactor-an-in-silico-strategy-using-model-reduction-and-bayesian-optimization
#16
Mohammad Mehrian, Yann Guyot, Ioannis Papantoniou, Simon Olofsson, Maarten Sonnaert, Ruth Misener, Liesbet Geris
In regenerative medicine, computer models describing bioreactor processes can assist in designing optimal process conditions leading to robust and economically viable products. In this study, we started from a (3D) mechanistic model describing the growth of neotissue, comprised of cells and extracellular matrix, in a perfusion bioreactor set-up influenced by the scaffold geometry, flow-induced shear stress and a number of metabolic factors. Subsequently, we applied model reduction by reformulating the problem from a set of partial differential equations into a set of ordinary differential equations...
December 4, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29205274/production-of-cellulosic-organic-acids-via-synthetic-fungal-consortia
#17
Scott A Scholz, Ian Graves, Jeremy J Minty, Xiaoxia Nina Lin
Consolidated bioprocessing is a potential breakthrough technology for reducing costs of biochemical production from lignocellulosic biomass. Production of cellulase enzymes, saccharification of lignocellulose and conversion of the resulting sugars into a chemical of interest occur simultaneously within a single bioreactor. In this study, synthetic fungal consortia composed of the cellulolytic fungus Trichoderma reesei and the production specialist Rhizopus delemar demonstrated conversion of microcrystalline cellulose (MCC) and alkaline pre-treated corn stover to fumaric acid in a fully consolidated manner without addition of cellulase enzymes or expensive supplements such as yeast extract...
December 2, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29205113/immobilization-techniques-applied-to-the-development-of-biocatalysts-for-the-synthesis-of-nucleoside-analogue-derivatives
#18
Jorge Abel Trelles, Maria Jose Lapponiab
BACKGROUND: Nucleoside analogue (NAs) derivatives comprise a large family of pharmaceuticals clinically used as antitumoral and antiviral compounds. Originally, the production of NAs involved chemical synthesis, but a greener bioproduction alternative exists and involves the use of enzymes that catalyze transglycosylation reactions between modified purinic or pyrimidinic bases and sugars. To be considered as an option for industrial application, it is vital to immobilize these biocatalysts...
December 3, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/29201141/valorization-of-pyrolysis-water-a-biorefinery-side-stream-for-1-2-propanediol-production-with-engineered-corynebacterium-glutamicum
#19
Julian Lange, Felix Müller, Kerstin Bernecker, Nicolaus Dahmen, Ralf Takors, Bastian Blombach
Background: A future bioeconomy relies on the efficient use of renewable resources for energy and material product supply. In this context, biorefineries have been developed and play a key role in converting lignocellulosic residues. Although a holistic use of the biomass feed is desired, side streams evoke in current biorefinery approaches. To ensure profitability, efficiency, and sustainability of the overall conversion process, a meaningful valorization of these materials is needed...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29201138/implementation-and-use-of-cloud-based-electronic-lab-notebook-in-a-bioprocess-engineering-teaching-laboratory
#20
Erin M Riley, Holly Z Hattaway, P Arthur Felse
Background: Electronic lab notebooks (ELNs) are better equipped than paper lab notebooks (PLNs) to handle present-day life science and engineering experiments that generate large data sets and require high levels of data integrity. But limited training and a lack of workforce with ELN knowledge have restricted the use of ELN in academic and industry research laboratories which still rely on cumbersome PLNs for recordkeeping. We used LabArchives, a cloud-based ELN in our bioprocess engineering lab course to train students in electronic record keeping, good documentation practices (GDPs), and data integrity...
2017: Journal of Biological Engineering
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