Optimization of rifamycin B fermentation in shake flasks via a machine-learning-based approach.

Abstract:

:Rifamycin B is an important polyketide antibiotic used in the treatment of tuberculosis and leprosy. We present results on medium optimization for Rifamycin B production via a barbital insensitive mutant strain of Amycolatopsis mediterranei S699. Machine-learning approaches such as Genetic algorithm (GA), Neighborhood analysis (NA) and Decision Tree technique (DT) were explored for optimizing the medium composition. Genetic algorithm was applied as a global search algorithm while NA was used for a guided local search and to develop medium predictors. The fermentation medium for Rifamycin B consisted of nine components. A large number of distinct medium compositions are possible by variation of concentration of each component. This presents a large combinatorial search space. Optimization was achieved within five generations via GA as well as NA. These five generations consisted of 178 shake-flask experiments, which is a small fraction of the search space. We detected multiple optima in the form of 11 distinct medium combinations. These medium combinations provided over 600% improvement in Rifamycin B productivity. Genetic algorithm performed better in optimizing fermentation medium as compared to NA. The Decision Tree technique revealed the media-media interactions qualitatively in the form of sets of rules for medium composition that give high as well as low productivity.

journal_name

Biotechnol Bioeng

authors

Bapat PM,Wangikar PP

doi

10.1002/bit.20056

subject

Has Abstract

pub_date

2004-04-20 00:00:00

pages

201-8

issue

2

eissn

0006-3592

issn

1097-0290

journal_volume

86

pub_type

杂志文章
  • Accurate kinetic parameter estimation during progress curve analysis of systems with endogenous substrate production.

    abstract::We have identified an error in the published integral form of the modified Michaelis-Menten equation that accounts for endogenous substrate production. The correct solution is presented and the error in both the substrate concentration, S, and the kinetic parameters Vm , Km , and R resulting from the incorrect solutio...

    journal_title:Biotechnology and bioengineering

    pub_type: 信件

    doi:10.1002/bit.23181

    authors: Goudar CT

    更新日期:2011-10-01 00:00:00

  • Interactions between animal cells and gas bubbles: The influence of serum and pluronic F68 on the physical properties of the bubble surface.

    abstract::We describe a method by which the degree of bubble saturation can be determined by measuring the velocity of single bubbles at different heights from the bubble source in pure water containing increasing concentrations of surfactants. The highest rising velocities were measured in pure water. Addition of surfactants c...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260430603

    authors: Jordan M,Eppenberger HM,Sucker H,Widmer F,Einsele A

    更新日期:1994-03-15 00:00:00

  • Glucose-containing polymer rings enable fed-batch operation in microtiter plates with parallel online measurement of scattered light, fluorescence, dissolved oxygen tension, and pH.

    abstract::Bioprocesses operated in batch mode can induce adverse effects like overflow metabolism, substrate inhibition, osmotic inhibition, oxygen limitation, and catabolite repression. To avoid these adverse effects, fed-batch is the predominant operation mode in industrial production. Nevertheless, screening for optimal prod...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.27077

    authors: Habicher T,Czotscher V,Klein T,Daub A,Keil T,Büchs J

    更新日期:2019-09-01 00:00:00

  • Cellulase immobilized on poly-L-glutamic acid.

    abstract::Cellulase (Cellulosin AC-8) was immobilized on poly-L-glutamic acid. This immobilized cellulase (IC) is water soluble in the neutral and alkaline solutions, where IC has the activity, while IC can be made insoluble by lowering the pH so that it can be recovered from the reaction mixture with its activity. The optimum ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260290203

    authors: Takeuchi T,Makino K

    更新日期:1987-02-01 00:00:00

  • Investigation of the TCA cycle and the glyoxylate shunt in Escherichia coli BL21 and JM109 using (13)C-NMR/MS.

    abstract::Acetate accumulation is a common problem observed in aerobic high cell density Escherichia coli cultures. A previous report has hypothesized that the glyoxylate shunt is active in a low acetate producer, E. coli BL21, and inactive in a high acetate producer, JM109. To further investigate this hypothesis, we now develo...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:

    authors: Noronha SB,Yeh HJ,Spande TF,Shiloach J

    更新日期:2000-05-05 00:00:00

  • Algal swimming velocities signal fatty acid accumulation.

    abstract::The use of microalgae for biofuel production will be beneficial to society if we can produce biofuels at large scales with minimal mechanical energy input in the production process. Understanding micro-algal physiological responses under variable environmental conditions in bioreactors is essential for the optimizatio...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.24619

    authors: Hansen TJ,Hondzo M,Mashek MT,Mashek DG,Lefebvre PA

    更新日期:2013-01-01 00:00:00

  • Characterization of recombinant strains of the Clostridium acetobutylicum butyrate kinase inactivation mutant: need for new phenomenological models for solventogenesis and butanol inhibition?

    abstract::Two metabolic engineering tools, namely gene inactivation and gene overexpression, were employed to examine the effects of two genetic modifications on the fermentation characteristics of Clostridium acetobutylicum. Inactivation of the butyrate kinase gene (buk) was examined using strain PJC4BK, while the combined eff...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:

    authors: Harris LM,Desai RP,Welker NE,Papoutsakis ET

    更新日期:2000-01-05 00:00:00

  • A non-chromatographic method for the removal of endotoxins from bacteriophages.

    abstract::The Ff filamentous bacteriophages show potential as a new class of therapeutics, displaying utility in materials science as well as pharmaceutical applications. These phages are produced by the infection of E. coli, a Gram-negative bacterium which unavoidably sheds endotoxins into the extracellular space during growth...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.25571

    authors: Branston SD,Wright J,Keshavarz-Moore E

    更新日期:2015-08-01 00:00:00

  • Biologically mediated mobilization of arsenic from granular ferric hydroxide in anaerobic columns fed landfill leachate.

    abstract::To gain insight on the fate of arsenic (As) from drinking water treatment residuals in landfills, the mobilization of arsenate adsorbed onto granular ferric hydroxide (GFH) was studied in continuous anaerobic columns fed with a synthetic landfill leachate. The release of As was compared in biologically active and abio...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.22021

    authors: Cortinas I,Sierra-Alvarez R,Field JA

    更新日期:2008-12-15 00:00:00

  • Destruction and formation of toxins by one bacterial species affect biodegradation by a second species.

    abstract::Two strains of Pseudomonas able to grow on phenol or p-nitrophenol (PNP) were isolated from sewage. Pseudomonas sp. PN101 mineralized and formed nitrite from PNP but did not mineralize phenol, and Pseudomonas sp. PH111 mineralized phenol but not PNP. Phenol increased the lag period before Pseudomonas sp. PN101 grew on...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260330706

    authors: Murakami Y,Alexander M

    更新日期:1989-02-20 00:00:00

  • Investigation of particle-functionalized tissue engineering scaffolds using X-ray tomographic microscopy.

    abstract::A low-density, porous chitosan/poly-(dl-lactide-co-glycolide) (PLGA) microparticle composite scaffold was produced by thermally induced phase separation followed by lyophilization, to provide a bicontinuous microstructure potentially suitable for tissue engineering and locally controlled drug release. PLGA particles w...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.21796

    authors: Nygaard JV,Andersen MØ,Howard KA,Foss M,Bünger C,Kjems J,Besenbacher F

    更新日期:2008-07-01 00:00:00

  • Particle-tethered NADH for production of methanol from CO(2) catalyzed by coimmobilized enzymes.

    abstract::Efficient cofactor regeneration and reuse are highly desired for many important biotransformation applications. Here we show for the first time that cofactor NAD(H) covalently attached to micro particles, which can be easily recovered and reused, effectively mediated multistep reactions catalyzed by enzymes that were ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.21584

    authors: El-Zahab B,Donnelly D,Wang P

    更新日期:2008-02-15 00:00:00

  • Effects of calcium on development of anaerobic acidogenic biofilms.

    abstract::Anerobic biofilms with dominantly acidogenic bacteria were grown in fixed-bed recycle reactors. The influence of calcium concentration in the culture medium on biofilm mass accumulation, immobilized calcium concentration, and biofilm-specific activity was investigated. The results indicate that the biofilm mass accumu...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260450305

    authors: Huang J,Pinder KL

    更新日期:1995-02-05 00:00:00

  • Enhancing ligand-protein binding in affinity thermoprecipitation: elucidation of spacer effects

    abstract::Copolymers of N-isopropylacrylamide and N-acryloyl amino acid spacers of varying chain length were synthesized. p-Aminobenzamidine (PABA) was chemically linked to the pendant carboxyl groups of these polymers to obtain thermoprecipitating affinity polymers. The inhibition constant (Ki) of these polymers for trypsin de...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/(sici)1097-0290(19990820)64:4<418::aid-bit

    authors: Vaidya AA,Lele BS,Kulkarni MG,Mashelkar RA

    更新日期:1999-08-20 00:00:00

  • Feeding heterogeneity in ciliate populations: Effects of culture age and nutritional state.

    abstract::We have used a novel approach in conjunction with flow cytometry to quantify the biological heterogeneity of populations of the ciliate Tetrahymena pyriformis. It was found that the rate of particle uptake of exponentially growing cells is not uniform among cells and partially correlated with cell size. The physiologi...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260430505

    authors: Hatzis C,Srienc F,Fredrickson AG

    更新日期:1994-03-05 00:00:00

  • Esterification reactions of lipase in reverse micelles.

    abstract::The activities of lipase from Candida cylindracea and Rhizopus delemar have been investigated in water/AOT/iso-octane reverse micellar media through the use of two esterification reactions: fatty acid-alcohol esterification and glyceride synthesis. Such media promotes the occurrence of these two lipase-catalyzed react...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260350807

    authors: Hayes DG,Gulari E

    更新日期:1990-04-05 00:00:00

  • Kinetics of ethanol inhibition in alcohol fermentation.

    abstract::The inhibitory effect of ethanol on yeast growth and fermentation has been studied for the strain Saccharomyces cerevisiae ATCC No. 4126 under anaerobic batch conditions. The results obtained reveal that there is no striking difference between the response of growth and ethanol fermentation. Two kinetic models are als...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260270311

    authors: Luong JH

    更新日期:1985-03-01 00:00:00

  • Engineering of molecular and cellular biocatalysts: selected contributions by James E. Bailey.

    abstract::James (Jay) E. Bailey was a pioneer in biotechnology and biochemical engineering. During his 30 years in academia he made seminal contributions to many fields of chemical engineering science, including catalysis and reaction engineering, bioprocess engineering, mathematical modeling of cellular processes, recombinant ...

    journal_title:Biotechnology and bioengineering

    pub_type: 传,历史文章,杂志文章

    doi:10.1002/bit.10404

    authors: Dordick JS,Khosla C

    更新日期:2002-09-05 00:00:00

  • Nitrogen compounds in wine during its biological aging by two flor film yeasts: An approach to accelerated biological aging of dry sherry-type wines.

    abstract::Urea, ammonium, and free amino acid contents were quantified in biological aging of a young wine under two flor film forming yeast strains, Saccharomyces cerevisiae race capensis and S. cerevisiae race bayanus, and compared. Cell viability in the film was different for the two yeast strains. Thus, capensis maintained ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/(SICI)1097-0290(19970120)53:2<159::AID-BIT

    authors: Mauricio JC,Ortega JM

    更新日期:1997-01-20 00:00:00

  • Reactive oxygen species induced by shear stress mediate cell death in Bacillus subtilis.

    abstract::Exposure of Bacillus subtilis to a shear rate of 1,482/s leads to a rapid loss of cell viability after 10 h of growth. Biochemical and molecular evidences provided below strongly suggest that cell death under high shear results from an apoptosis-like process similar to that described in eukaryotes, with activation of ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.20835

    authors: Sahoo S,Rao KK,Suraishkumar GK

    更新日期:2006-05-05 00:00:00

  • Immobilization of yeast cells containing beta-galactosidase.

    abstract::Cultural conditions optimum for beta-galactosidase production by Saccharomyces anamensis are pH 4.5, temperature 26 +/- 2 degrees C, and 30 h of incubation period. Addition of lactose at 24 h fermentation greatly increase the level of enzyme. Optimum pHl, temperature, pH stability, and thermostability of yeast beta-ga...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260240810

    authors: Banerjee M,Chakrabarty A,Majumdar SK

    更新日期:1982-08-01 00:00:00

  • The relationship between fiber-porosity and cellulose digestibility in steam-exploded Pinus radiata.

    abstract::Steam explosion after sulphur dioxide impregnation of wood chips is an effective method for improving the enzymatic digestibility of cellulose in the softwood Pinus radiata. Digestibility of pretreated fiber was progressively increased by altering the conditions of steam explosion. With increasing digestibility, there...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260310509

    authors: Wong KK,Deverell KF,Mackie KL,Clark TA,Donaldson LA

    更新日期:1988-04-05 00:00:00

  • Gelatin interpenetration in poly N-isopropylacrylamide network reduces the compressive modulus of the scaffold: A property employed to mimic hepatic matrix stiffness.

    abstract::The progression of liver disease from normal to cirrhotic state is characterized by modulation of the stiffness of the extracellular matrix (ECM). Mimicking this modulation in vitro scaffold could provide a better insight into hepatic cell behavior. In this study, interpenetrating poly(N-isopropylacrylamide-co-gelatin...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.27218

    authors: Sarkar J,Kamble SC,Patil R,Kumar A,Gosavi SW

    更新日期:2020-02-01 00:00:00

  • Visualizing lignin coalescence and migration through maize cell walls following thermochemical pretreatment.

    abstract::Plant cell walls are composed primarily of cellulose, hemicelluloses, lignins, and pectins. Of these components, lignins exhibit unique chemistry and physiological functions. Although lignins can be used as a product feedstock or as a fuel, lignins are also generally seen as a barrier to efficient enzymatic breakdown ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.21959

    authors: Donohoe BS,Decker SR,Tucker MP,Himmel ME,Vinzant TB

    更新日期:2008-12-01 00:00:00

  • Enzymatic glucosylation of hydrophobic alcohols in organic medium by the reverse hydrolysis reaction using almond-beta-D-glucosidase.

    abstract::Alkyl beta-D-glucosides were synthesized from D-glucose and alcohols by reverse hydrolysis using the commercially available almond beta-D-glucosidase in 9:1 (v/v) acetonitrile-water medium. The main characteristics of this enzyme-catalyzed glucosylation were established by using 2-hydroxybenzyl alcohol. The reaction i...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260460204

    authors: Vic G,Biton J,Le Beller D,Michel JM,Thomas D

    更新日期:1995-04-20 00:00:00

  • Activated sludge system design for large variations or organic loading.

    abstract::An aeration tank/sedimentation tank system is considered for large variations of organic loading. In this case, it is important to take into account the variability of the characteristics describing the oxidation of activated sludge as well as its sedimentation. The minimum cost of the treatment system is also evaluat...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260241105

    authors: Vasiliev VB,Vavilin VA

    更新日期:1982-11-01 00:00:00

  • Recovery of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) from Ralstonia eutropha cultures with non-halogenated solvents.

    abstract::Reduced downstream costs, together with high purity recovery of polyhydroxyalkanoate (PHA), will accelerate the commercialization of high quality PHA-based products. In this work, a process was designed for effective recovery of the copolymer poly(hydroxybutyrate-co-hydroxyhexanoate) (P(HB-co-HHx)) containing high lev...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.24713

    authors: Riedel SL,Brigham CJ,Budde CF,Bader J,Rha C,Stahl U,Sinskey AJ

    更新日期:2013-02-01 00:00:00

  • Application of solid-liquid TPPBs to the production of L-phenylacetylcarbinol from benzaldehyde using Candida utilis.

    abstract::The biotransformation of benzaldehyde and glucose to L-phenylacetylcarbinol (PAC) using Candida utilis was demonstrated in a solid-liquid two-phase partitioning bioreactor (TPPB) with the aim of reducing substrate, product, and by-product toxicity via sequestration. Previous work in the field had used octanol as the s...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.22839

    authors: Khan TR,Daugulis AJ

    更新日期:2010-11-01 00:00:00

  • A new bioproduction route for a novel antimicrobial peptide.

    abstract::Beta defensins are antimicrobial peptides (AMPs) with a broad spectrum antimicrobial behavior against pathogens while having minimal tendency to incur pathogen resistance. Human β-defensin 28 (hBD28) is a strongly cationic AMP and hence hypothesized to be highly effective in permeabilizing negatively-charged pathogen ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.22970

    authors: Tay DK,Rajagopalan G,Li X,Chen Y,Lua LH,Leong SS

    更新日期:2011-03-01 00:00:00

  • Lipase activity in vesicular systems: characterization of candida cylindracea lipase and its activity in polymerizable dialkylammonium surfactant vesicles.

    abstract::Lipase from Candida cylindracea (CCL) was incorporated into polymerizable positively charged dialkylammonium bromide surfactant vesicles. The enzyme was incorporated by the use of the dehydration-rehydration method or by incubation. In the latter case, trapping efficiencies of up to 100% could be obtained. Activities ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260420207

    authors: Mosmuller EW,Franssen MC,Engbersen JF

    更新日期:1993-06-20 00:00:00