Model-based analysis of the role of biological, hydrological and geochemical factors affecting uranium bioremediation.

Abstract:

:Uranium contamination is a serious concern at several sites motivating the development of novel treatment strategies such as the Geobacter-mediated reductive immobilization of uranium. However, this bioremediation strategy has not yet been optimized for the sustained uranium removal. While several reactive-transport models have been developed to represent Geobacter-mediated bioremediation of uranium, these models often lack the detailed quantitative description of the microbial process (e.g., biomass build-up in both groundwater and sediments, electron transport system, etc.) and the interaction between biogeochemical and hydrological process. In this study, a novel multi-scale model was developed by integrating our recent model on electron capacitance of Geobacter (Zhao et al., 2010) with a comprehensive simulator of coupled fluid flow, hydrologic transport, heat transfer, and biogeochemical reactions. This mechanistic reactive-transport model accurately reproduces the experimental data for the bioremediation of uranium with acetate amendment. We subsequently performed global sensitivity analysis with the reactive-transport model in order to identify the main sources of prediction uncertainty caused by synergistic effects of biological, geochemical, and hydrological processes. The proposed approach successfully captured significant contributing factors across time and space, thereby improving the structure and parameterization of the comprehensive reactive-transport model. The global sensitivity analysis also provides a potentially useful tool to evaluate uranium bioremediation strategy. The simulations suggest that under difficult environments (e.g., highly contaminated with U(VI) at a high migration rate of solutes), the efficiency of uranium removal can be improved by adding Geobacter species to the contaminated site (bioaugmentation) in conjunction with the addition of electron donor (biostimulation). The simulations also highlight the interactive effect of initial cell concentration and flow rate on U(VI) reduction.

journal_name

Biotechnol Bioeng

authors

Zhao J,Scheibe TD,Mahadevan R

doi

10.1002/bit.23096

subject

Has Abstract

pub_date

2011-07-01 00:00:00

pages

1537-48

issue

7

eissn

0006-3592

issn

1097-0290

journal_volume

108

pub_type

杂志文章
  • Diffusion of lactate and ammonium in relation to growth of Geotrichum candidum at the surface of solid media.

    abstract::Geotrichum candidum was cultivated at the surface of solid model media containing peptone to simulate the composition of Camembert cheese. The surface growth of G. candidum induced the diffusion of substrates from the core to the rind and the diffusion of produced metabolites from the rind to the core. In the range of...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.20100

    authors: Aldarf M,Fourcade F,Amrane A,Prigent Y

    更新日期:2004-07-05 00:00:00

  • Simulations of host-plasmid interactions in Escherichia coli: Copy number, promoter strength, and ribosome binding site strength effects on metabolic activity and plasmid gene expression.

    abstract::A mechanistically detailed single-cell model E. coli B/r-A was adapted to simulate the effects of vector presence on cell metabolism. Competition for RNA polymerase between chromosome and plasmid DNA is explicitly included. Distribution of active ribosomes among chromosome- and plasmid-derived messenger RNA, another k...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260290305

    authors: Peretti SW,Bailey JE

    更新日期:1987-02-01 00:00:00

  • Estimation of the true growth yield and maintenance coefficient for yoghurt cultures.

    abstract::Point and 95% confidence interval estimates of the true growth yield and maintenance coefficient are reported for four pure cultures andtwo mixed cultures of Lactobacillus bulgaricus and Streptococcus thermophilus grown anaerobically on 3% nonfat dry milk using batch followed by fed batch culture. An improved method o...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260280619

    authors: Oner MD,Erickson LE,Yang SS

    更新日期:1986-06-01 00:00:00

  • Production of recombinant proteins using multiple-copy gene integration in high-cell-density fermentations of Ralstonia eutropha.

    abstract::We have previously reported the development of a novel protein expression system based on Ralstonia eutropha. In this study we report on the influence of gene copynumber on recombinant protein expression in R. eutropha. We compare recombinant gene stability and expression levels of chromosomal integration with a plasm...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.10756

    authors: Srinivasan S,Barnard GC,Gerngross TU

    更新日期:2003-10-05 00:00:00

  • Accelerated homology-directed targeted integration of transgenes in Chinese hamster ovary cells via CRISPR/Cas9 and fluorescent enrichment.

    abstract::Targeted gene integration into site-specific loci can be achieved in Chinese hamster ovary (CHO) cells via CRISPR/Cas9 genome editing technology and the homology-directed repair (HDR) pathway. The low efficiency of HDR often requires antibiotic selection, which limits targeted integration of multiple genes at multiple...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.26002

    authors: Lee JS,Grav LM,Pedersen LE,Lee GM,Kildegaard HF

    更新日期:2016-11-01 00:00:00

  • Determination of cells' water membrane permeability: unexpected high osmotic permeability of Saccharomyces cerevisiae.

    abstract::Water permeability (Lp), calculated from the volume variations of cells subjected to an osmotic shock, is classically used to characterize cell membrane properties. In this work, we have shown the importance of the kind of mixing reactor used to measure the Lp parameter. A mathematical model including the mixing time ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/(SICI)1097-0290(19971005)56:1<62::AID-BIT7

    authors: de Marañón IM,Gervais P,Molin P

    更新日期:1997-10-05 00:00:00

  • Improvement of Escherichia coli microaerobic oxygen metabolism by Vitreoscilla hemoglobin: New insights from NAD(P)H fluorescence and culture redox potential.

    abstract::On-line NAD(P)H fluorescence and culture redox potential (CRP) measurements were utilized to investigate the role of Vitreoscilla hemoglobin (VHb) in perturbing oxygen metabolism of microaerobic Escherichia coli Batch cultures of a VHb-synthesizing E. coli strain and the iso-genic control under fully aerated condition...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260470309

    authors: Tsai PS,Rao G,Bailey JE

    更新日期:1995-08-05 00:00:00

  • Towards the industrialization of new biosurfactants: Biotechnological opportunities for the lactone esterase gene from Starmerella bombicola.

    abstract::Although sophorolipids (SLs) produced by S. bombicola are a real showcase for the industrialization of microbial biosurfactants, some important drawbacks are associated with this efficient biological process, e.g., the simultaneous production of acidic and lactonic SLs. Depending on the application, there is a require...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.25815

    authors: Roelants SL,Ciesielska K,De Maeseneire SL,Moens H,Everaert B,Verweire S,Denon Q,Vanlerberghe B,Van Bogaert IN,Van der Meeren P,Devreese B,Soetaert W

    更新日期:2016-03-01 00:00:00

  • Hydrolysis of lactose by free and immobilized beta-galactosidase from Thermus sp. strain T2.

    abstract::The hydrolysis of lactose by a beta-galactosidase from the thermophilic microorganism Thermus sp. strain T2, both in solution and immobilized on a commercial silica-alumina, has been studied. The enzyme has been previously produced by Escherichia coli JM101 harboring the plasmid pBGT1, which contains the codifying gen...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.10466

    authors: Ladero M,Perez MT,Santos A,Garcia-Ochoa F

    更新日期:2003-01-20 00:00:00

  • Unified kinetic treatment for growth on dual nutrients.

    abstract::This paper presents a new formulation for the analysis of growth kinetics on multiple nutrients. The baseline for the theory is the concept that a noninteractive growth process occurs among perfectly substitutable nutrients if the locus of points of the substrate concentrations producing equal growth rate is linear. A...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260440203

    authors: Haas CN

    更新日期:1994-06-20 00:00:00

  • Fractional factorial design to investigate stromal cell regulation of macrophage plasticity.

    abstract::Understanding the regulatory networks which control specific macrophage phenotypes is essential in identifying novel targets to correct macrophage mediated clinical disorders, often accompanied by inflammatory events. Since mesenchymal stromal cells (MSCs) have been shown to play key roles in regulating immune functio...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.25282

    authors: Barminko JA,Nativ NI,Schloss R,Yarmush ML

    更新日期:2014-11-01 00:00:00

  • Yield stress of pretreated corn stover suspensions using magnetic resonance imaging.

    abstract::Cellulose fibers in water form networks that give rise to an apparent yield stress, especially at high solids contents. Measuring the yield stress and correlating it with fiber concentration is important for the biomass and pulp industries. Understanding how the yield stress behaves at high solids concentrations is cr...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.23197

    authors: Lavenson DM,Tozzi EJ,McCarthy MJ,Powell RL

    更新日期:2011-10-01 00:00:00

  • Mathematical modeling and optimization of cellulase protein production using Trichoderma reesei RL-P37.

    abstract::The enzyme cellulase, a multienzyme complex made up of several proteins, catalyzes the conversion of cellulose to glucose in an enzymatic hydrolysis-based biomass-to-ethanol process. Production of cellulase enzyme proteins in large quantities using the fungus Trichoderma reesei requires understanding the dynamics of g...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/(sici)1097-0290(1999)66:1<1::aid-bit1>3.0.

    authors: Tholudur A,Ramirez WF,McMillan JD

    更新日期:1999-01-01 00:00:00

  • Physiologic mechanisms of sequential products synthesis in 1,3-propanediol fed-batch fermentation by Klebsiella pneumoniae.

    abstract::The glycerol fed-batch fermentation by Klebsiella pneumoniae CGMCC 1.6366 exhibited the sequential synthesis of products, including acetate, 1,3-propanediol (1,3-PD), 2,3-butanediol, ethanol, succinate, and lactate. The dominant flux distribution was shifted from acetate formation to 1,3-PD formation in early- exponen...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.21830

    authors: Zheng ZM,Xu YZ,Liu HJ,Guo NN,Cai ZZ,Liu DH

    更新日期:2008-08-01 00:00:00

  • Bioprocess considerations for expanded-bed chromatography of crude canola extract: sample preparation and adsorbent reuse.

    abstract::Compared to the conventional microbial and mammalian systems, transgenic plants produce proteins in a different matrix. This provides opportunities and challenges for downstream processing. In the context of the plant host Brassica napus (canola), this work addresses the bioprocessing challenges of solid fractionation...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.10524

    authors: Bai Y,Glatz CE

    更新日期:2003-03-30 00:00:00

  • Milligram scale production of potent recombinant small interfering RNAs in Escherichia coli.

    abstract::Small interfering RNAs (siRNAs) are invaluable research tools for studying gene functions in mammalian cells. siRNAs are mainly produced by chemical synthesis or by enzymatic digestion of double-stranded RNA (dsRNA) produced in vitro. Recently, bacterial cells, engineered with ectopic plant viral siRNA binding protein...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.26740

    authors: Kaur G,Cheung HC,Xu W,Wong JV,Chan FF,Li Y,McReynolds L,Huang L

    更新日期:2018-09-01 00:00:00

  • Biosorption of lead and nickel by biomass of marine algae.

    abstract::Screening tests of different marine algae biomas types revealed a high passive biosorptive uptake of lead up to 270 mg Pb/g of biomass in some brown marine algae. Members of the order Fucales perfomed particularly well in this descending sequence: Fucus > Ascophyllum > Sargassum. Although decreasing the swelling of we...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260431102

    authors: Holan ZR,Volesky B

    更新日期:1994-05-01 00:00:00

  • Growth and fermentation characteristics of new selected strains of Saccharomyces at high temperatures and high cell densities.

    abstract::Maintenance of high cell viability was the main characteristic of our new strains of thermotolerant Saccharomyces. Total sugar conversion to ethanol was observed for sugarcane juice fermentation at 38-40 degrees C in less than 10 h and without continuous aeration of the culture. Invertase activity differed among the s...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260370606

    authors: Laluce C,Palmieri MC,Lopes da Cruz RC

    更新日期:1991-03-15 00:00:00

  • Effect of hydration on the morphology of enzyme powder.

    abstract::We report the first direct images of the hydration of protein powders. Using an environmental scanning electron microscope (ESEM) we have taken a series of micrographs of a region of the enzyme (subtilisin) power whilst hydrating the sample. In addition, the sample has been viewed during exposure to toluene vapors. Th...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260391114

    authors: Roziewski K,Russell AJ

    更新日期:1992-05-01 00:00:00

  • Biomanufacturing of value-added products from oils or fats: A case study on cellular and fermentation engineering of Yarrowia lipolytica.

    abstract::The United States produces more than 10 million tons of waste oils and fats each year. This paper aims to establish a new biomanufacturing platform that converts waste oils or fats into a series of value-added products. Our research employs the oleaginous yeast Yarrowia lipolytica as a case study for citric acid (CA) ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.27685

    authors: Liu N,Soong YV,Mirzaee I,Olsen A,Yu P,Wong HW,Xie D

    更新日期:2021-01-20 00:00:00

  • Behavior of spores of Penicillium roquefortii during fed-batch bioconversion of octanoic acid into 2-heptanone.

    abstract::The bioconversion of octanoic acid into 2-heptanone by spores of Penicillium roquefortii is performed using a fed-batch technique with pH control by addition of the liquid substrate itself. The early stage of this process takes place with a high bioconversion rate and high yield. These values then decrease as a result...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260440606

    authors: Larroche C,Besson I,Gros JB

    更新日期:1994-09-05 00:00:00

  • A synthetic enzymatic pathway for extremely thermophilic acetone production based on the unexpectedly thermostable acetoacetate decarboxylase from Clostridium acetobutylicum.

    abstract::One potential advantage of an extremely thermophilic metabolic engineering host (T opt ≥ 70°C) is facilitated recovery of volatile chemicals from the vapor phase of an active fermenting culture. This process would reduce purification costs and concomitantly alleviate toxicity to the cells by continuously removing solv...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.26829

    authors: Zeldes BM,Straub CT,Otten JK,Adams MWW,Kelly RM

    更新日期:2018-12-01 00:00:00

  • Experimental measurement of particle size distribution and voidage in an expanded bed adsorption system.

    abstract::This paper presents an experimental analysis of matrix bead size distribution and voidage variations with axial height in an expanded bed adsorption system. Use of a specially constructed expanded bed with side ports has enabled sampling from within the expanded bed along the vertical axis. Particles removed from with...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/1097-0290(20000920)69:6<648::aid-bit9>3.0.

    authors: Willoughby NA,Hjorth R,Titchener-Hooker NJ

    更新日期:2000-09-20 00:00:00

  • Packaging guest proteins into the encapsulin nanocompartment from Rhodococcus erythropolis N771.

    abstract::The encapsulin nanocompartment from Rhodococcus erythropolis N771 (Reencapsulin) was expressed and purified in wild-type and C-terminally His-tagged forms. Negative-stained transmission electron microscopy, field-flow fractionation combined with multi-angle light scattering and dynamic light scattering analyses showed...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.25322

    authors: Tamura A,Fukutani Y,Takami T,Fujii M,Nakaguchi Y,Murakami Y,Noguchi K,Yohda M,Odaka M

    更新日期:2015-01-01 00:00:00

  • Study of drop and bubble sizes in a simulated mycelial fermentation broth of up to four phases.

    abstract::The mean sizes and size distributions of air bubbles and viscous castor oil drops were studied in a salt-rich aqueous solution (medium), first separately, and then simultaneously as a three-phase system. The dispersion was created in a 150-mm-diameter stirred tank equipped with a Rushton turbine, and the sizes were me...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/(sici)1097-0290(20000720)69:2<213::aid-bit

    authors: Galindo E,Pacek AW,Nienow AW

    更新日期:2000-07-20 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

  • New reaction system for hydrocarbon oxidation by chloroperoxidase.

    abstract::A novel reaction system was developed to maximize the catalytic efficiency of chloroperoxidase (CPO, from Caldariomyces fumago) toward the oxidation of hydrocarbons. The reaction system consisted of an organic/aqueous emulsion comprising pure substrate and aqueous buffer supplemented with the surfactant dioctyl sulfos...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.20769

    authors: Park JB,Clark DS

    更新日期:2006-05-05 00:00:00

  • Biomass evolution in porous media and its effects on permeability under starvation conditions.

    abstract::The purpose of this study was to understand bacteria profile modification and its applications in subsurface biological operations such as biobarrier formation, in situ bioremediation, and microbial-enhanced oil recovery. Biomass accumulation and evolution in porous media were investigated both experimentally and theo...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/(sici)1097-0290(20000705)69:1<47::aid-bit6

    authors: Kim DS,Fogler HS

    更新日期:2000-07-05 00:00:00

  • A comparison of mathematical model predictions to experimental measurements for growth and recombinant protein production in induced cultures of Escherichia coli.

    abstract::Recombinant cell growth and protein synthesis by a recombinant Escherichia coli under various inducing conditions are compared to the predictions of a mathematical model. The mathematical model used was a combination of two literature models: (1) an empirical kinetic model for recombinant growth and product formation ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260360204

    authors: Betenbaugh MJ,Dhurjati P

    更新日期:1990-06-20 00:00:00

  • Tuning biphenyl dioxygenase for extended substrate specificity.

    abstract::Highly substituted polychlorinated biphenyls (PCBs) are known to be very resistant to aerobic biodegradation, particularly the initial attack by biphenyl dioxygenase. Functional evolution of the substrate specificity of biphenyl dioxygenase was demonstrated by DNA shuffling and staggered extension process (StEP) of th...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/(sici)1097-0290(19990605)63:5<544::aid-bit

    authors: Brühlmann F,Chen W

    更新日期:1999-06-05 00:00:00