@article{vasquez-garay_teixeira mendonca_peretti_2018, title={Chemoenzymatic lignin valorization: Production of epoxidized pre-polymers using Candida antarctica lipase B}, volume={112}, ISSN={["1879-0909"]}, DOI={10.1016/j.enzmictec.2018.01.007}, abstractNote={An innovative chemoenzymatic catalytic system for functionalizing lignin from Organosolv and Kraft pulping processes to obtain oxirane rings was investigated. Novozym435 (immobilized C. antarctica lipase B: CalB) was used to catalyze the peroxidation of caprylic acid to peroxycaprylic acid, which in turn reacted with unsaturated CC bonds to form the oxirane ring. The conversion of OH groups to oxirane rings (epoxides) reached 90% and 55% after 12 h for the two processes, respectively. The residual enzyme activity over the time course of the reactions indicated transient denaturing due to association with the lignin substrate (10–50%) as well as irreversible denaturation due to exposure to hydrogen peroxide. Functionalized lignin has potential applications in the production of epoxy adhesive resins, and chemoenzymatic synthesis represents a “greener” pathway to this synthesis.}, journal={ENZYME AND MICROBIAL TECHNOLOGY}, author={Vasquez-Garay, Francisco and Teixeira Mendonca, Regis and Peretti, Steven W.}, year={2018}, month={May}, pages={6–13} }
 @article{barton_carrier_segura_fierro_park_lamb_escalona_peretti_2018, title={Ni/HZSM-5 catalyst preparation by deposition-precipitation. Part 2. Catalytic hydrodeoxygenation reactions of lignin model compounds in organic and aqueous systems}, volume={562}, ISSN={0926-860X}, url={http://dx.doi.org/10.1016/J.APCATA.2018.06.012}, DOI={10.1016/J.APCATA.2018.06.012}, abstractNote={Nickel metal supported on HZSM-5 (zeolite) is a promising catalyst for lignin depolymerization. In this work, the ability of catalysts prepared via deposition-precipitation (DP) to perform hydrodeoxygenation (HDO) on two lignin model compounds in organic and aqueous solvents was evaluated; guaiacol in dodecane and 2-phenoxy-1-phenylethanol (PPE) in aqueous solutions. All Ni/HZSM-5 catalysts were capable of guaiacol HDO into cyclohexane at 523 K. The role of the HZSM-5 acid sites was confirmed by comparison with Ni/SiO2 (inert support) which exhibited incomplete deoxygenation of guaiacol due to the inability to perform the cyclohexanol dehydration step. The catalyst prepared with 15 wt% Ni, a DP time of 16 h, and a calcination temperature of 673 K (Ni(15)/HZSM-5 DP16_Cal673), performed the guaiacol conversion with the greatest selectivity towards HDO products, with an intrinsic rate ratio (HDO rate to conversion rate) of 0.31, and 90% selectivity to cyclohexane. Catalytic activity and selectivity of Ni/HZSM-5 (15 wt%) in aqueous environments (water and 0.1 M NaOH solution) was confirmed using PPE reactions at 523 K. After 30 min reaction time in water, Ni/HZSM-5 exhibited ∼100% conversion of PPE, and good yield of the desired products; ethylbenzene and phenol (∼35% and 23% of initial carbon, respectively). Ni/HZSM-5 in NaOH solution resulted in significantly higher ring saturation compared to the Ni/HZSM-5 in water or the NaOH solution control.}, journal={Applied Catalysis A: General}, publisher={Elsevier BV}, author={Barton, R.R. and Carrier, M. and Segura, C. and Fierro, J.L.G. and Park, S. and Lamb, H.H. and Escalona, N. and Peretti, S.W.}, year={2018}, month={Jul}, pages={294–309} }
 @article{barton_carrier_segura_fierro_escalona_peretti_2017, title={Ni/HZSM-5 catalyst preparation by deposition-precipitation. Part 1. Effect of nickel loading and preparation conditions on catalyst properties}, volume={540}, ISSN={["1873-3875"]}, DOI={10.1016/j.apcata.2017.03.040}, abstractNote={Nickel metal supported on HZSM-5 (zeolite) is a promising catalyst for lignin depolymerization. In this work, Ni/HZSM-5 catalysts were synthesized via deposition-precipitation (DP) and characterized. The effect of synthesis parameters; including nickel loading, DP time (synthesis contact time), and calcination temperature, on catalyst properties were studied. N2 and CO2 adsorption techniques were used to look at textural properties and confirmed the existence of lamellar species generated from DP. X-ray diffraction (XRD) confirmed that nickel metal was present on the support after reduction and passivation of the catalyst. Temperature programmed reduction showed that all the catalyst preparations were reducible at 733 K after 4 h, and that the DP method formed a mixture of Ni2+ species on the support. Transmission electron microscopy, XRD, and H2 chemisorption were used to determine approximate particle size and dispersion of nickel metal. From all the preparations, the 15 wt% Ni/HZSM-5 catalyst with long DP time (16 h) and low calcination temperature (673 K), exhibited the most favorable particle size (∼5 nm) and dispersion (7%).}, journal={APPLIED CATALYSIS A-GENERAL}, author={Barton, R. R. and Carrier, M. and Segura, C. and Fierro, J. L. G. and Escalona, N. and Peretti, S. W.}, year={2017}, month={Jun}, pages={7–20} }
 @article{peretti_barton_mendonca_2016, title={Lignin as feedstock for fibers and chemicals}, volume={43}, journal={Commercializing biobased products: opportunities, challenges, benefits, and risks}, author={Peretti, S. W. and Barton, R. and Mendonca, R. T.}, year={2016}, pages={132–165} }
 @article{eby_peretti_2015, title={Characterization, performance, and applications of a yeast surface display-based biocatalyst}, volume={5}, ISSN={["2046-2069"]}, DOI={10.1039/c4ra16304d}, abstractNote={Yeast surface display (YSD) of two lipases. Measured expression level and copy number. Synthetic and hydrolytic activity comparable to commercial lipase. Cost analysis of YSD system vs. commercial formulations.}, number={25}, journal={RSC ADVANCES}, author={Eby, J. M. and Peretti, S. W.}, year={2015}, pages={19166–19175} }
 @article{eby_peretti_2015, title={Performance in synthetic applications of a yeast surface display-based biocatalyst}, volume={5}, ISSN={["2046-2069"]}, DOI={10.1039/c5ra04039f}, abstractNote={Organic synthesis with surface-displayed lipase: alkyl esters of fatty acids. Compared performance to commercial preparations. Catalyst is reusable and stable up to 50–60 °C. Kinetics of surface-displayed synthesis of butyl decanoate.}, number={39}, journal={RSC ADVANCES}, author={Eby, J. M. and Peretti, S. W.}, year={2015}, pages={30425–30432} }
 @article{cushing_peretti_2013, title={Enzymatic processing of renewable glycerol into value-added glycerol carbonate}, volume={3}, ISSN={["2046-2069"]}, DOI={10.1039/c3ra43811b}, abstractNote={Increased production of biodiesel has led to excess glycerol production worldwide, which has resulted in a significant drop in glycerol prices. Glycerol carbonate is a multifunctional compound used as chemical intermediates, solvents, additives and monomers. In this study, the enzymatic synthesis of glycerol carbonate from glycerol and a dialkyl carbonate was investigated. Glycerol carbonate was formed when reacting glycerol with dimethyl carbonate, diethyl carbonate or dibutyl carbonate in the presence of Candida antarctica lipase B (Novozym 435), using tert-butanol as a solvent. Nearly 100% glycerol conversion was reached after 12 h, with glycerol carbonate being the primary product. The effects of reaction parameters including solvent choice and biocatalyst loading were also examined. The highest activity was found at restricted water conditions and when using tert-butanol as a solvent.}, number={40}, journal={RSC ADVANCES}, author={Cushing, Kerri A. and Peretti, Steven W.}, year={2013}, pages={18596–18604} }
 @article{panneerselvam_sharma-shivappa_kolar_ranney_peretti_2013, title={Potential of ozonolysis as a pretreatment for energy grasses}, volume={148}, ISSN={["1873-2976"]}, DOI={10.1016/j.biortech.2013.08.129}, abstractNote={This study investigated the effect of ozonolysis on Miscanthus × giganteus, Miscanthus sinensis 'Gracillimus', Saccharum arundinaceum and Saccharum ravennae, collectively referred to as 'energy grasses'. Studies were conducted at three different ozone concentrations (40, 50 and 58 mg/l) using two ozone flow configurations - uni-directional and reversed flow. Pretreatment conditions for each variety were optimized based on lignin content and glucan recovery in ozonated solids. Results showed that ozonolysis was effective in removing up to 59.9% lignin without cellulose degradation. However, subsequent hydrolysis of pretreated solids with Cellic® CTec2 at 0.06 g/g raw biomass provided glucan conversion lower than untreated samples suggesting enzyme inhibition by lignin degradation products formed during ozonolysis. Future studies investigating hydrolysis efficiency of washed pretreated solids with higher enzyme loadings are therefore warranted to optimize the hydrolysis process and make it functionally feasible.}, journal={BIORESOURCE TECHNOLOGY}, author={Panneerselvam, Anushadevi and Sharma-Shivappa, Ratna R. and Kolar, Praveen and Ranney, Thomas and Peretti, Steven}, year={2013}, month={Nov}, pages={242–248} }
 @article{athalye_sharma-shivappa_peretti_kolar_davis_2013, title={Producing biodiesel from cottonseed oil using Rhizopus oryzae ATCC #34612 whole cell biocatalysts: Culture media and cultivation period optimization}, volume={17}, ISSN={0973-0826}, url={http://dx.doi.org/10.1016/J.ESD.2013.03.009}, DOI={10.1016/J.ESD.2013.03.009}, abstractNote={The effect of culture medium composition and cultivation time on biodiesel production by Rhizopus oryzae ATCC #34612 whole cell catalysts, immobilized on novel rigid polyethylene biomass supports, was investigated. Supplementation of the medium with carbon sources led to higher lipase activity and increased the biomass immobilized on the BSPs. Statistical analysis indicates that a cultivation period of 72 h in a basal medium supplemented with both cottonseed oil and glucose is optimal for biodiesel production by R. oryzae, resulting in a fatty acid methyl ester (FAME) yield of 27.9 wt.% (228.2 g/L).}, number={4}, journal={Energy for Sustainable Development}, publisher={Elsevier BV}, author={Athalye, Sneha and Sharma-Shivappa, Ratna and Peretti, Steven and Kolar, Praveen and Davis, Jack P.}, year={2013}, month={Aug}, pages={331–336} }
 @article{gray_peretti_lamb_2013, title={Real-time monitoring of high-gravity corn mash fermentation using in situ raman spectroscopy}, volume={110}, ISSN={["1097-0290"]}, DOI={10.1002/bit.24849}, abstractNote={Abstract}, number={6}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={Gray, Steven R. and Peretti, Steven W. and Lamb, H. Henry}, year={2013}, month={Jun}, pages={1654–1662} }
 @inproceedings{cooper_bullard_peretti_ollis_2012, title={Application of plagiarism screening software in the chemical engineering curriculum}, booktitle={ASEE Annual Conference Proceedings}, author={Cooper, M. and Bullard, L. and Peretti, S. and Ollis, D.}, year={2012} }
 @article{bullard_niehues_peretti_white_2005, title={Web-based delivery of ChE design projects}, volume={39}, number={3}, journal={Chemical Engineering Education}, author={Bullard, L. G. and Niehues, P. K. and Peretti, S. W. and White, S. H}, year={2005}, pages={194–199} }
 @article{dannels_anson_bullard_peretti_2003, title={Challenges in learning communication skills in chemical engineering}, volume={52}, DOI={10.1080/03634520302454}, abstractNote={Communication across the curriculum initiatives face multiple curricular and pedagogical challenges that are especially appropriate for investigation within a scholarship of teaching and learning framework. Using qualitative methodologies, this study examined technical classes that emphasize speaking and writing. Four learning issues emerged in student reflection logs: integrating multidisciplinary information, managing varied audiences and feedback, aligning content and communication tasks, and addressing interpersonal team issues. Data indicated that students were resistant toward the incursion of communication in their engineering classes. Through reflective practice, teachers and cross-curricular consultants came to understand and address that resistance.}, number={1}, journal={Communication Education}, author={Dannels, D. P. and Anson, C. M. and Bullard, Lisa and Peretti, S.}, year={2003}, pages={50–56} }
 @inproceedings{dannels_berardinelle_anson_bullard_kleid_kmeic_peretti_2003, title={Instruction and assessment of multidisciplinary teaming skills in senior design}, booktitle={Proceedings of the American Association of Engineering Education, USA}, author={Dannels, D. P. and Berardinelle, P. and Anson, C. and Bullard, L. and Kleid, N. and Kmeic, D. and Peretti, S.}, year={2003} }
 @article{peretti_tompkins_goodall_michaels_2002, title={Extraction of 4-nitrophenol from 1-octanol into aqueous solution in a hollow fiber liquid contactor}, volume={195}, ISSN={["1873-3123"]}, DOI={10.1016/S0376-7388(01)00566-X}, abstractNote={p-Nitrophenol (PNP) was extracted from 1-octanol into an aqueous buffered solution using membrane-supported extraction in hollow fiber liquid contactors (HFLCs) containing hydrophobic, microporous polypropylene fibers. PNP is a weak acid and in aqueous solution may dissociate to form nitrophenolate ion (PNP−), that has negligible solubility in 1-octanol. The ratio of the two species in aqueous solution is governed by pH; therefore, the overall mass transfer coefficient based on solvent phase concentrations was determined as a function of pH. The extraction of PNP is a four-step process, consisting of diffusion across the solvent boundary layer, diffusion through the solvent-filled membrane, reaction (dissociation) at the solvent/aqueous interface, and diffusion across the aqueous boundary layer. The reaction step is assumed much faster than the others; a model of the mass transfer capabilities of the system is presented based on this assumption. The overall mass transfer coefficients were determined experimentally by recirculating the solvent phase through the shell space of a HFLC and the aqueous phase through the fibers. The model closely predicts the experimentally measured trends of the overall mass transfer coefficient.}, number={2}, journal={JOURNAL OF MEMBRANE SCIENCE}, author={Peretti, SW and Tompkins, CJ and Goodall, JL and Michaels, AS}, year={2002}, month={Jan}, pages={193–202} }
 @article{miller_peretti_2002, title={Toluene bioconversion to p-hydroxybenzoate by fed-batch cultures of recombinant Pseudomonas putida}, volume={77}, ISSN={["1097-0290"]}, DOI={10.1002/bit.10071}, abstractNote={Abstract}, number={3}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={Miller, ES and Peretti, SW}, year={2002}, month={Feb}, pages={340–351} }
 @inproceedings{peretti_shepherd_clayton_proffitt_kaplan_wander_2000, title={Membrane biotreatment of VOC-laden air}, booktitle={Proceedings of the Air & Waste Management Association's Annual Conference & Exhibition}, author={Peretti, S. W. and Shepherd, R. D. and Clayton, R. K. and Proffitt, D. E. and Kaplan, N. and Wander, O. D.}, year={2000}, pages={2526–2539} }
 @article{peretti_judge_hindmarch_2000, title={Safety and tolerability considerations: tricyclic antidepressants vs. selective serotonin reuptake inhibitors}, volume={101}, ISSN={["1600-0447"]}, DOI={10.1111/j.1600-0447.2000.tb10944.x}, abstractNote={Peretti S, Judge R, Hindmarch I. Safety and tolerability considerations: tricyclic antidepressants vs. selective serotonin reuptake inhibitors. Acta Psychiatr Scand 2000: 101: 17–25. © Munksgaard 2000.}, journal={ACTA PSYCHIATRICA SCANDINAVICA}, author={Peretti, S and Judge, R and Hindmarch, I}, year={2000}, pages={17–25} }
 @article{miller_peretti_1999, title={Bioconversion of toluene to p-hydroxybenzoate via the construction and characterization of a recombinant Pseudomonas putida}, volume={1}, ISSN={["1463-9270"]}, DOI={10.1039/a901383k}, abstractNote={Biocatalytic production of p-hydroxybenzoate (HBA) provides improved regiospecificity over Kolbe–Schmitt carboxylation of phenol while achieving significant source reductions in the generation of waste and byproducts. Construction of the organism for HBA production was accomplished through two classical approaches for the engineering of organisms in the production of specialty chemicals: (1) strain enhancement through chemical mutagenesis to create a mutant Pseudomonas putida, EM2839, deficient in HBA degradation, and (2) hybrid pathway construction through the recruitment of genes encoding the toluene-4-monooxygenase (T4MO) (tmoABCDE), p-cresol methylhyroxylase (pchCF), and p-hydroxybenzaldehyde dehydrogenase (phbz) genes from existing pathways and stably incorporating them into the organism through the use of mini-Tn5 transposon systems.Time course measurements of HBA production by resting cells of P. putida EM2878 in batch cultures revealed that T4MO conversion of toluene to p-creseol, the first step in the pathway, significantly constrained the carbon flux in the pathway, yielding a maximum rate of HBA production of 1.61 ± 0.15 nmol min–1 mg protein–1. In fed-batch culture, toluene conversion to HBA by P. putida EM2878 showed absolute selectivity for para-hydroxybenzoate production. Maximum HBA concentrations of 35 mg l–1 were achieved in about 28 hours of operation. However, the rate of HBA production was significantly less than that observed during batch studies. The slower rate of HBA production observed in the fed-batch culture was correlated with the degradation of specific T4MO polypeptides.}, number={3}, journal={GREEN CHEMISTRY}, author={Miller, ES and Peretti, SW}, year={1999}, month={Jun}, pages={143–152} }
 @misc{peretti_thomas_shepherd_1999, title={Bioreactor process for the continuous removal of organic compounds from a vapor phase process stream}, volume={5,954,858}, number={1999 Sept. 21}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Peretti, S. W. and Thomas, S. M. and Shepherd, R. D., Jr.}, year={1999} }
 @article{thomas_peretti_1998, title={Continuous culture dynamics for aniline metabolism by Pseudomonas sp. CIT1}, volume={58}, ISSN={["1097-0290"]}, DOI={10.1002/(SICI)1097-0290(19980405)58:1<1::AID-BIT1>3.0.CO;2-J}, abstractNote={Inhibition by toxic substrates enables multiple steady states to arise in biodegradation systems. This phenomenon was investigated for the continuous metabolism of aniline by Pseudomonas sp. CIT1. Differences of various metabolic parameters between the two growth regimes (uninhibited and inhibited) and the transient response to a step-up in dilution rate were determined. Regulatory mechanisms consistent with the experimental evidence are proposed. Aniline is the transcriptional inducer of a metabolic pathway that converts aniline to TCA cycle intermediates. The suite of enzymes is coordinately expressed from a single promoter. We followed the level of the pathway mRNA using a fragment containing the catechol 2,3 dioxygenase gene (andioxB) and monitored the pathway enzyme activity using catechol 2,3 dioxygenase (C23D). The inhibited regime resulted in a 60% lower growth yield, near constant levels of C23D monomer, but a 50% reduction in the specific activity of C23D, increased RNA synthesis rates (total and aniline pathway mRNA), and elevated RNA decay rates. Elucidation of regulatory mechanisms indicates that C23D is noncompetitively inhibited by aniline and subject to feedback inhibition by 2-hydroxymuconic semialdehyde (HMS). During uninhibited growth regime operation, metabolism of HMS is the rate-limiting step; in contrast, conversion of aniline to catechol limits growth in the inhibited regime.}, number={1}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={Thomas, SM and Peretti, SW}, year={1998}, month={Apr}, pages={1–12} }
 @article{matsui_randell_peretti_davis_boucher_1998, title={Coordinated clearance of periciliary liquid and mucus from airway surfaces}, volume={102}, ISSN={["0021-9738"]}, DOI={10.1172/JCI2687}, abstractNote={Airway surface liquid is comprised of mucus and an underlying, watery periciliary liquid (PCL). In contrast to the well-described axial transport of mucus along airway surfaces via ciliary action, theoretical analyses predict that the PCL is nearly stationary. Conventional and confocal microscopy of fluorescent microspheres and photoactivated fluorescent dyes were used with well-differentiated human tracheobronchial epithelial cell cultures exhibiting spontaneous, radial mucociliary transport to study the movements of mucus and PCL. These studies showed that the entire PCL is transported at approximately the same rate as mucus, 39.2+/-4.7 and 39.8+/-4.2 micrometer/sec, respectively. Removing the mucus layer reduced PCL transport by > 80%, to 4.8+/-0.6 micrometer/sec, a value close to that predicted from theoretical analyses of the ciliary beat cycle. Hence, the rapid movement of PCL is dependent upon the transport of mucus. Mucus-dependent PCL transport was spatially uniform and exceeded the rate expected for pure frictional coupling with the overlying mucus layer; hence, ciliary mixing most likely accelerates the diffusion of momentum from mucus into the PCL. The cephalad movement of PCL along airway epithelial surfaces makes this mucus-driven transport an important component of salt and water physiology in the lung in health and disease.}, number={6}, journal={JOURNAL OF CLINICAL INVESTIGATION}, author={Matsui, H and Randell, SH and Peretti, SW and Davis, CW and Boucher, RC}, year={1998}, month={Sep}, pages={1125–1131} }
 @article{goodall_peretti_1998, title={Dynamic modeling of meta- and para-nitrobenzoate metabolism by a mixed co-immobilized culture of Comamonas spp. JS46 and JS47}, volume={59}, DOI={10.1002/(SICI)1097-0290(19980820)59:4<507::AID-BIT14>3.3.CO;2-1}, abstractNote={A model describing the transient activity of a mixed immobilized culture of Comamonas spp. JS46 and JS47 growing on mixed substrates is presented. The transient periods considered are those following changes in the feed carbon source, which alternated between meta- and para-nitrobenzoate. The feed profile alternately starved one of the species in the mixed culture. The response of the system, as quantified by the reactor effluent substrate concentrations, is dictated by the activity of the biomass and the appropriate biochemical pathway. As detailed mechanistic pathway information is not available, respirometry has been used to characterize both facets of activity. Two parameters were introduced: Ψ representing pathway activity and Γ representing biomass activity; a detailed description of the analysis is included. The model is compared to experimental investigation of the system and describes the reactor response well. The agreement between model and experiment suggests the usefulness of oxygen kinetics as global measurements to describe complex systems when mechanistic detail is not available. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59: 507–516, 1998.}, number={4}, journal={Biotechnology and Bioengineering}, author={Goodall, J. L. and Peretti, S. W.}, year={1998}, pages={507–516} }
 @article{beaudoin_bryers_cunningham_peretti_1998, title={Mobilization of broad host range plasmid from Pseudomonas putida to established biofilm of Bacillus azotoformans. I. Experiments}, volume={57}, DOI={10.1002/(SICI)1097-0290(19980205)57:3<272::AID-BIT3>3.0.CO;2-E}, abstractNote={A strain of Pseudomonas putida harboring plasmids RK2 and pDLB101 was exposed to a pure culture biofilm of Bacillus azotoformans grown in a rotating annular reactor under three different concentrations of the limiting nutrient, succinate. Experimental results demonstrated that the broad host range RSF1010 derivative pDLB101 was transferred to and expressed by B. azotoformans. At the lower concentrations, donor mediated plasmid transfer increased with increasing nutrient levels, but the highest nutrient concentration yielded the lowest rate of donor to recipient plasmid transfer. For transconjugant initiated transfer, the rate of transfer increased with increasing nutrient concentrations for all cases. At the lower nutrient concentrations, the frequency of plasmid transfer was higher between donors and recipients than between transconjugants and recipients. The reverse was true at the highest succinate concentration. The rates and frequencies of plasmid transfer by mobilization were compared to gene exchange by retrotransfer. The initial rate of retrotransfer was slower than mobilization, but then increased dramatically. Retrotransfer produced a plasmid transfer frequency more than an order of magnitude higher than simple mobilization.}, number={3}, journal={Biotechnology and Bioengineering}, author={Beaudoin, D. L. and Bryers, J. D. and Cunningham, A. B. and Peretti, S. W.}, year={1998}, pages={272–279} }
 @article{beaudoin_bryers_cunningham_peretti_1998, title={Mobilization of broad host range plasmid from Pseudomonas putida to established biofilm of Bacillus azotoformans. II. Modeling}, volume={57}, DOI={10.1002/(SICI)1097-0290(19980205)57:3<280::AID-BIT4>3.3.CO;2-E}, abstractNote={A strain of Pseudomonas putida that harbors plasmids RK2 and pDLB101 was exposed to a pure culture biofilm of Bacillus azotoformans grown in a rotating annular reactor. Transfer of the RK2 mobilizable pDLB101 plasmid to B. azotoformans was monitored over a 4-day period. Experimental results demonstrated that the broad host range, RSF1010 derivative pDLB101 was transferred to and expressed by B. azotoformans. In the companion article to this work, the rate of plasmid transfer was quantified as a function of the limiting nutrient, succinate, and as a function of the mechanism of transfer. A biofilm process simulation program (AQUASIM) was modified to analyze resultant experimental data. Although the AQUASIM package was not designed to simulate or predict genetic events in biofilms, modification of the rate process dynamics allowed successful modeling of plasmid transfer. For the narrow range of substrate concentrations used in these experiments, nutrient level had only a slight effect on the rate and extent of plasmid transfer in biofilms. However, further simulations using AQUASIM revealed that under nutrient poor conditions, the number of transconjugants appearing in the biofilm was limited. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 57: 280–286, 1998.}, number={3}, journal={Biotechnology and Bioengineering}, author={Beaudoin, D. L. and Bryers, J. D. and Cunningham, A. B. and Peretti, S. W.}, year={1998}, pages={280–286} }
 @article{goodall_thomas_spain_peretti_1998, title={Operation of mixed-culture immobilized cell reactors for the metabolism of meta- and para-nitrobenzoate by Comamonas sp. JS46 and Comamonas sp. JS47}, volume={59}, ISSN={["0006-3592"]}, DOI={10.1002/(SICI)1097-0290(19980705)59:1<21::AID-BIT4>3.0.CO;2-V}, abstractNote={The treatment of meta- and para-nitrobenzoic acid in an industrial wastestream by Comamonas sp. JS46 and Comamonas sp. JS47 is investigated. The most important feature of the wastestream is the constantly changing concentration ratio of the two isomers. The most extreme occurrence is considered here: the complete change in feed carbon source from one isomer to the other. A series of immobilized cell airlift reactor experiments are described to examine the operation and response of the system to these changes in the feed carbon source. Separate reactors containing each species immobilized are compared with a reactor containing both species immobilized within the same bead, and to a reactor containing both species with each species confined to separate beads. On the basis of response time necessary to recover the appropriate activity, the reactor containing both species immobilized within the same bead offers the most effective arrangement. Interactions occurring between the two organisms in the coimmobilized system, mediated by the nitrobenzoate metabolites, are discussed relative to the improved response of this arrangement. Copyright 1998 John Wiley & Sons, Inc.}, number={1}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={Goodall, JL and Thomas, SM and Spain, JC and Peretti, SW}, year={1998}, month={Jul}, pages={21–27} }
 @article{huang_peretti_bryers_1994, title={EFFECTS OF INDUCER LEVELS ON A RECOMBINANT BACTERIAL BIOFILM FORMATION AND GENE-EXPRESSION}, volume={16}, ISSN={["0141-5492"]}, DOI={10.1007/bf00128622}, number={9}, journal={BIOTECHNOLOGY LETTERS}, author={HUANG, CT and PERETTI, SW and BRYERS, JD}, year={1994}, month={Sep}, pages={903–908} }
 @article{huang_peretti_bryers_1994, title={EFFECTS OF MEDIUM CARBON-TO-NITROGEN RATIO ON BIOFILM FORMATION AND PLASMID STABILITY}, volume={44}, ISSN={["1097-0290"]}, DOI={10.1002/bit.260440310}, abstractNote={Abstract}, number={3}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={HUANG, CT and PERETTI, SW and BRYERS, JD}, year={1994}, month={Jul}, pages={329–336} }
 @article{smolko_peretti_1994, title={Stimulation of berberine secretion and growth in cell cultures of Thalictrum minus}, volume={14}, DOI={10.1007/bf00233776}, abstractNote={An endo-pectate lyase (PL; EC 4.2.2.2), originally cloned fiom the phytopathogenic bacterium Erwinia chrysanthemi EC16, was expressed in recA (-) E. coli strain DK1, purified to a single band by isoelectric focusing and used to induce berberine production in established plant suspension cultures of Thalictrum minus L. subsp. saxatile. Addition of 10(-9)M pectate lyase c (PLc) stimulated berberine production and enhanced secretion of the alkaloid into the medium. A lower concentration of PLc, 10(-11)M, stimulated a transient two-fold increase in cell growth rate relative to untreated cultures. Parallel changes in L-phenylalanine ammonia lyase (PAL; EC 4.3.1.5) activity with the rate of berberine synthesis and the inverse relationship between cell growth and berberine synthesis imply that berberine synthesis is stress-related in this cell line.}, number={2/3}, journal={Plant Cell Reports}, author={Smolko, D. D. and Peretti, S. W.}, year={1994}, pages={131–136} }
 @article{kuhn_peretti_ollis_1993, title={ACID INHIBITION OF IMMOBILIZED CELLS - QUANTITATIVE COMPARISON OF MODEL AND EXPERIMENT}, volume={39}, ISSN={["0273-2289"]}, DOI={10.1007/bf02919006}, journal={APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY}, author={KUHN, R and PERETTI, S and OLLIS, D}, year={1993}, pages={401–413} }
 @article{peretti_bryers_1993, title={Effects of biofilm formation on plasmid segregational stability and expression.}, volume={223}, journal={NATO ASI Series, Series E: Applied Sciences}, author={Peretti, S. W. and Bryers, J. D}, year={1993}, pages={181–198} }
 @article{huang_peretti_bryers_1993, title={PLASMID RETENTION AND GENE-EXPRESSION IN SUSPENDED AND BIOFILM CULTURES OF RECOMBINANT ESCHERICHIA-COLI DH5 ALPHA(PMJR1750)}, volume={41}, ISSN={["1097-0290"]}, DOI={10.1002/bit.260410207}, abstractNote={Abstract}, number={2}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={HUANG, CT and PERETTI, SW and BRYERS, JD}, year={1993}, month={Jan}, pages={211–220} }
 @article{padukone_peretti_ollis_1992, title={ANALYSIS OF PRODUCTIVITY IN LYSIS-DEFICIENT LAMBDA EXPRESSION SYSTEMS}, volume={40}, ISSN={["1097-0290"]}, DOI={10.1002/bit.260400608}, abstractNote={Abstract}, number={6}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={PADUKONE, N and PERETTI, SW and OLLIS, DF}, year={1992}, month={Sep}, pages={697–704} }
 @article{padukone_peretti_ollis_1992, title={Bacteriophage lambda expression systems for enhanced recombinant protein production}, volume={210}, journal={NATO ASI Series, Series E: Applied Sciences}, author={Padukone, N. and Peretti, S. W. and Ollis, D. F}, year={1992}, pages={367–372} }
 @article{padukone_peretti_ollis_1992, title={CHARACTERIZATION OF THE MUTANT LYTIC STATE IN LAMBDA EXPRESSION SYSTEMS}, volume={39}, ISSN={["0006-3592"]}, DOI={10.1002/bit.260390402}, abstractNote={Abstract}, number={4}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={PADUKONE, N and PERETTI, SW and OLLIS, DF}, year={1992}, month={Feb}, pages={369–377} }
 @article{tompkins_michaels_peretti_1992, title={REMOVAL OF P-NITROPHENOL FROM AQUEOUS-SOLUTION BY MEMBRANE-SUPPORTED SOLVENT-EXTRACTION}, volume={75}, ISSN={["0376-7388"]}, DOI={10.1016/0376-7388(92)85069-u}, abstractNote={p-Nitrophenol was extracted from aqueous solution into 1-octanol via membrane solvent extraction, using a hydrophobic, microporous-wall, polypropylene hollow fiber module. The system was operated with the aqueous phase flowing through the fiber lumens and the octanol flowing through the shell space. The overall mass transfer coefficient for the extraction was measured and analyzed in terms of individual resistance to mass transfer. The average value for the overall mass transfer coefficient was 6.5×10−4 cm/sec. The resistance to mass transfer of the tube side boundary layer and membrane were found to be controlling, while the shell side boundary layer resistance was negligible. The tube side boundary layer resistance measured in these experiments agreed well with a prediction based on the Sherwood number correlation for well developed laminar flow in tubes. The experimentally measured membrane permability to solute transport was substantially smaller than that predicted for solute diffusion through octanol occupying the membrane pores; flow maldistribution and channeling of solvent in the shell space is believed to be the most probable cause of this disparity. The results support the belief that membrane solvent extraction may be a technically and economically feasible means for selectively removing organic solutes from very dilute aqueous waste streams characteristic of many chemical plant effluents.}, number={3}, journal={JOURNAL OF MEMBRANE SCIENCE}, author={TOMPKINS, CJ and MICHAELS, AS and PERETTI, SW}, year={1992}, month={Dec}, pages={277–292} }
 @article{huang_peretti_bryers_1992, title={Use of flow cell reactors to quantify biofilm formation kinetics}, volume={6}, DOI={10.1007/bf02439342}, abstractNote={A parallel plate flow cell reactor is introduced and used to evaluate cell adhesion and biofilm formation kinetics for four different bacterial strains of the species,E. coli. The reactor allows biofilm growth under defined, well-controlled fluid dynamics while providing continuous observations and direct sampling of biofilm for biological, chemical and physical analyses as well as immunofluorescent labeling.}, number={3}, journal={Biotechnology Techniques}, author={Huang, C. T. and Peretti, S. W. and Bryers, J. D.}, year={1992}, pages={193–198} }
 @misc{michaels_peretti_tompkins_1991, title={Bioreactor process for continuous removal of organic toxicants and other oleophilc solutes from an aqueous process stream}, volume={4,988,443}, number={1991 Jan. 29}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Michaels, A. and Peretti, S. and Tompkins, C.}, year={1991} }
 @article{wood_peretti_1991, title={CONSTRUCTION OF A SPECIALIZED-RIBOSOME VECTOR FOR CLONED-GENE EXPRESSION IN ESCHERICHIA-COLI}, volume={38}, ISSN={["1097-0290"]}, DOI={10.1002/bit.260380811}, abstractNote={Abstract}, number={8}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={WOOD, TK and PERETTI, SW}, year={1991}, month={Oct}, pages={891–906} }
 @article{wood_peretti_1991, title={EFFECT OF CHEMICALLY-INDUCED, CLONED-GENE EXPRESSION ON PROTEIN-SYNTHESIS IN ESCHERICHIA-COLI}, volume={38}, ISSN={["0006-3592"]}, DOI={10.1002/bit.260380410}, abstractNote={Abstract}, number={4}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={WOOD, TK and PERETTI, SW}, year={1991}, month={Aug}, pages={397–412} }
 @article{kuhn_peretti_ollis_1991, title={MICROFLUORIMETRIC ANALYSIS OF SPATIAL AND TEMPORAL PATTERNS OF IMMOBILIZED CELL-GROWTH}, volume={38}, ISSN={["1097-0290"]}, DOI={10.1002/bit.260380404}, abstractNote={Abstract}, number={4}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={KUHN, RH and PERETTI, SW and OLLIS, DF}, year={1991}, month={Aug}, pages={340–352} }
 @article{wood_peretti_1990, title={DEPRESSION OF PROTEIN SYNTHETIC CAPACITY DUE TO CLONED-GENE EXPRESSION IN ESCHERICHIA-COLI}, volume={36}, ISSN={["1097-0290"]}, DOI={10.1002/bit.260360902}, abstractNote={Abstract}, number={9}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={WOOD, TK and PERETTI, SW}, year={1990}, month={Nov}, pages={865–878} }
 @article{wood_kuhn_peretti_1990, title={Enhanced plasmid stability through post-segregational killing of plasmid-free cells}, volume={4}, DOI={10.1007/bf00156608}, number={1}, journal={Biotechnology Techniques}, author={Wood, T. K. and Kuhn, R. H. and Peretti, S. W.}, year={1990}, pages={39–44} }
 @article{padukone_peretti_ollis_1990, title={LAMBDA VECTORS FOR STABLE CLONED GENE-EXPRESSION}, volume={6}, ISSN={["8756-7938"]}, DOI={10.1021/bp00004a008}, abstractNote={Abstract}, number={4}, journal={BIOTECHNOLOGY PROGRESS}, author={PADUKONE, N and PERETTI, SW and OLLIS, DF}, year={1990}, pages={277–282} }
 @article{peretti_bailey_lee_1989, title={TRANSCRIPTION FROM PLASMID GENES, MACROMOLECULAR STABILITY, AND CELL-SPECIFIC PRODUCTIVITY IN ESCHERICHIA-COLI CARRYING COPY NUMBER MUTANT PLASMIDS}, volume={34}, ISSN={["1097-0290"]}, DOI={10.1002/bit.260340704}, abstractNote={Abstract}, number={7}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={PERETTI, SW and BAILEY, JE and LEE, JJ}, year={1989}, month={Oct}, pages={902–908} }
 @article{peretti_bailey_1988, title={TRANSIENT-RESPONSE SIMULATIONS OF RECOMBINANT MICROBIAL-POPULATIONS}, volume={32}, ISSN={["0006-3592"]}, DOI={10.1002/bit.260320403}, abstractNote={Abstract}, number={4}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={PERETTI, SW and BAILEY, JE}, year={1988}, month={Aug}, pages={418–429} }
 @article{peretti_bailey_1987, title={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}, volume={29}, ISSN={["1097-0290"]}, DOI={10.1002/bit.260290305}, abstractNote={Abstract}, number={3}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={PERETTI, SW and BAILEY, JE}, year={1987}, month={Feb}, pages={316–328} }
 @article{peretti_bailey_1986, title={MECHANISTICALLY DETAILED MODEL OF CELLULAR-METABOLISM FOR GLUCOSE-LIMITED GROWTH OF ESCHERICHIA-COLI B/R-A}, volume={28}, ISSN={["0006-3592"]}, DOI={10.1002/bit.260281111}, abstractNote={Abstract}, number={11}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={PERETTI, SW and BAILEY, JE}, year={1986}, month={Nov}, pages={1672–1689} }
 @article{bailey_dasilva_peretti_seo_srienc_1986, title={STUDIES OF HOST-PLASMID INTERACTIONS IN RECOMBINANT MICROORGANISMS}, volume={469}, ISSN={["0077-8923"]}, DOI={10.1111/j.1749-6632.1986.tb26498.x}, abstractNote={Plasmid genes redirect some components of cellular metabolism into synthesis of plasmid gene products and additional plasmids. The stoichiometric and kinetic implications of these host-plasmid interactions have been investigated theoretically and experimentally. Using known pathway energetics, maximum theoretical yield factors based on ATP, glucose, and O2 have been estimated for recombinant Escherichia coli and compared with corresponding estimates for host cells alone, indicating major changes in carbon and energetic stoichiometry in recombinant cells in cases of high cloned gene expression. The influence of the number of plasmids in recombinant E. coli has been experimentally characterized using a series of pMB1 derivatives stably propagated at copy numbers from 12 to 408. Recombinant cell growth rate declines monotonically as plasmid content increases as does efficiency of plasmid gene expression. A detailed metabolically structured single-cell model for E. coli has successfully simulated these trends. Interrelationships among number of plasmids per cell, induction of expression of a plasmid gene, and recombinant population growth rate have been experimentally delineated for Saccharomyces cerevisiae containing plasmid pLGSD5 and derivatives in which the 2-micron origin of replication has been replaced by a cloned ARS1 sequence or its deletion fragments. The CEN4 centromere sequence has been included in some of these plasmids to provide more regular segregation. Specific growth rate of these recombinant yeasts exhibits a maximum as a function of plasmid content, an effect attributed to the interplay between beneficial effects of the plasmid in selective medium and parasitic effects on metabolism at larger plasmid content or with more plasmid gene expression activity. The yeast strains investigated exhibit substantial segregational instability that was characterized using a rapid-flow cytometry measurement based upon single-cell deletion of E. coli beta-galactosidase activity in recombinant cells.}, journal={ANNALS OF THE NEW YORK ACADEMY OF SCIENCES}, author={BAILEY, JE and DASILVA, NA and PERETTI, SW and SEO, JH and SRIENC, F}, year={1986}, month={May}, pages={194–211} }