On the application of 'seeding' techniques in the primary separation of plasmid DNA from neutralised E-coli lysates

BACKGROUND: Initial extraction of plasmid DNA from Escherichia coli and its separation from host-derived contaminants is a difficult task to perform. Here, we examine the application of particle ‘seeding’ solid-liquid separation methods for primary recovery of plasmid DNA from neutralised alkaline cell lysates. RESULTS: Planting magnetic particle ‘seeds’ during cell lysis resulted in enhanced phase separation, facile magnetic separation of the floc, slight improvements in plasmid purity, but diminished plasmid recoveries. When CaCO3-coated low-density microspheres were seeded into flocs, phase separation was impaired, shear-induced floc damage and contamination of the plasmid liquor with genomic DNA and cell debris occurred, but plasmid DNA recovery was improved. Introduction of hydrophobic low-density microspheres into the floc dramatically improved floc stiffness, phase separation and flotation efficiency, and reduced the solids content in the plasmid liquor ten-fold. However, strong reinforcement of the cell debris lattice by these microspheres hindered plasmid release into the liquor beneath. CONCLUSION: By incorporating magnetic or buoyant seeds during cell lysis we have identified new routes for separation of shear-sensitive cell debris solids from crude plasmid containing liquors. Effective use of seeding approaches for difficult solid-liquid separation tasks will require evaluation of a wide range of seeds of varying architecture, size, shape, density and chemistry

Development of a simple intensified fermentation strategy for growth of Magnetospirillum gryphiswaldense MSR-1:Physiological responses to changing environmental conditions

The development of a simple pH-stat fed-batch fermentation strategy for the production of Magnetospirillum gryphiswaldense MSR-1 and magnetosomes (nanoscale magnetic organelles with biotechnological applications) is described. Flow cytometry was exploited as a powerful analytical tool for process development, enabling rapid monitoring of cell morphology, physiology and polyhydroxyalkanoate production. The pH-stat fed-batch growth strategy was developed by varying the concentrations of the carbon source (lactic acid) and the alternative electron acceptor (sodium nitrate) in the feed. Growth conditions were optimized on the basis of biomass concentration, cellular magnetism (indicative of magnetosome production), and intracellular iron concentration. The highest biomass concentration and cellular iron content achieved were an optical density at 565 nm of 15.5 (equivalent to 4.2 g DCW·L−1) and 33.1 mg iron·g−1 DCW, respectively. This study demonstrates the importance of analyzing bacterial physiology during fermentation development and will potentially aid the industrial production of magnetosomes, which can be used in a wide range of biotechnology and healthcare applications

Studies related to antibody fragment (Fab) production in Escherichia coli W3110 fed-batch fermentation processes using multiparameter flow cytometry

Background: Microbiology is important to industry therefore rapid and statistically representative measurements of cell physiological state, proliferation and viability are essential if informed decisions about fermentation bioprocess optimisation or control are to be made, since process performance will depend largely upon the number of metabolically active viable cells. Methods: Samples of recombinant Escherichia coli W3110, containing the gene for the D1.3 anti-lysozyme Fab fragment under the control of the lac based expression system, were taken at various stages from fed-batch fermentation processes and stained with a mixture of bis-(1, 3-dibutylbarbituric acid) trimethine oxonol and propidium iodide (PI/BOX). Where appropriate, measurements of dissolved oxygen tension (DOT), OD600nm and Fab concentration were made. Results: Depending on time of induction the maximum amount of Fab accumulating in the supernatant varied quite markedly from 1 – 4 μgml-1 as did subsequent cell physiological state with respect to PI/BOX staining with a concomitant drop in maximum biomass concentration. Conclusion: Depending on point of induction a 4 fold increase in Fab production could be achieved accompanied by a ~50% drop in maximum biomass concentration but with a higher proportion of viable cells as measured by multi-parameter flow cytometry

Multi-cycle recovery of lactoferrin and lactoperoxidase from crude whey using fimbriated high-capacity magnetic cation exchangers and a novel "rotor-stator" high-gradient magnetic separator

Cerium (IV) initiated "graft-from" polymerization reactions were employed to convert M-PVA magnetic particles into polyacrylic acid-fimbriated magnetic cation exchange supports displaying ultra-high binding capacity for basic target proteins. The modifications, which were performed at 25mg and 2.5g scales, delivered maximum binding capacities (Q) for hen egg white lysozyme in excess of 320mgg, combined with sub-micromolar dissociation constants (0.45-0.69μm) and "tightness of binding" values greater than 49Lg. Two batches of polyacrylic acid-fimbriated magnetic cation exchangers were combined to form a 5g pooled batch exhibiting Q values for lysozyme, lactoferrin, and lactoperoxidase of 404, 585, and 685mgg, respectively. These magnetic cation exchangers were subsequently employed together with a newly designed "rotor-stator" type HGMF rig, in five sequential cycles of recovery of lactoferrin and lactoperoxidase from 2L batches of a crude sweet bovine whey feedstock. Lactoferrin purification performance was observed to remain relatively constant from one HGMF cycle to the next over the five operating cycles, with yields between 40% and 49% combined with purification and concentration factors of 37- to 46-fold and 1.3- to 1.6-fold, respectively. The far superior multi-cycle HGMF performance seen here compared to that observed in our earlier studies can be directly attributed to the combined use of improved high capacity adsorbents and superior particle resuspension afforded by the new "rotor-stator" HGMS design. © 2013 Wiley Periodicals, Inc

In situ modification of chromatography adsorbents using cold atmospheric pressure plasmas

Efficient manufacturing of increasingly sophisticated biopharmaceuticals requires the development of new breeds of chromatographic materials featuring two or more layers, with each layer affording different functions. This letter reports the in situ modification of a commercial beaded anion exchange adsorbent using atmospheric pressure plasma generated within gas bubbles. The results show that exposure to He-O2 plasma in this way yields significant reductions in the surface binding of plasmid DNA to the adsorbent exterior, with minimal loss of core protein binding capacity; thus, a bi-layered chromatography material exhibiting both size excluding and anion exchange functionalities within the same bead is produced

Integrated system for temperature-controlled fast protein liquid chromatography. II. Optimized adsorbents and 'single column continuous operation'

Continued advance of a new temperature-controlled chromatography system, comprising a column filled with thermoresponsive stationary phase and a travelling cooling zone reactor (TCZR), is described. Nine copolymer grafted thermoresponsive cation exchangers (thermoCEX) with different balances of thermoresponsive (N-isopropylacrylamide), hydrophobic (N-tert-butylacrylamide) and negatively charged (acrylic acid) units were fashioned from three cross-linked agarose media differing in particle size and pore dimensions. Marked differences in grafted copolymer composition on finished supports were sourced to base matrix hydrophobicity. In batch binding tests with lactoferrin, maximum binding capacity (q max) increased strongly as a function of charge introduced, but became increasingly independent of temperature, as the ability of the tethered copolymer networks to switch between extended and collapsed states was lost. ThermoCEX formed from Sepharose CL-6B (A2), Superose 6 Prep Grade (B2) and Superose 12 Prep Grade (C1) under identical conditions displayed the best combination of thermoresponsiveness (q max,50°C/q max,10°C ratios of 3.3, 2.2 and 2.8 for supports 'A2', 'B2' and 'C1' respectively) and lactoferrin binding capacity (q max,50°C ~56, 29 and 45mg/g for supports 'A2', 'B2' and 'C1' respectively), and were selected for TCZR chromatography. With the cooling zone in its parked position, thermoCEX filled columns were saturated with lactoferrin at a binding temperature of 35°C, washed with equilibration buffer, before initiating the first of 8 or 12 consecutive movements of the cooling zone along the column at 0.1mm/s. A reduction in particle diameter (A2→B2) enhanced lactoferrin desorption, while one in pore diameter (B2→C1) had the opposite effect. In subsequent TCZR experiments conducted with thermoCEX 'B2' columns continuously fed with lactoferrin or 'lactoferrin+bovine serum albumin' whilst simultaneously moving the cooling zone, lactoferrin was intermittently concentrated at regular intervals within the exiting flow as sharp uniformly sized peaks. Halving the lactoferrin feed concentration to 0.5mg/mL, slowed acquisition of steady state, but increased the average peak concentration factor from 7.9 to 9.2. Finally, continuous TCZR mediated separation of lactoferrin from bovine serum albumin was successfully demonstrated. While the latter's presence did not affect the time to reach steady state, the average lactoferrin mass per peak and concentration factor both fell (respectively from 30.7 to 21.4mg and 7.9 to 6.3), and lactoferrin loss in the flowthrough between elution peaks increased (from 2.6 to 12.2mg). Fouling of the thermoCEX matrix by lipids conveyed into the feed by serum albumin is tentatively proposed as responsible for the observed drops in lactoferrin binding and recovery

A scalable biomanufacturing platform for bacterial magnetosomes

An integrated scalable platform for fermentative production and downstream processing of bacterial magnetosome products is advanced. Long magnetosome chains, high cellular magnetism, and low numbers of polyhydroxyalkanoate granules were obtained during the exponential growth phase of a two-stage continuous high cell density fermentation of M. gryphiswaldense MSR-1. Centrifugally concentrated 20% (w/v) suspensions of exponential phase cells were disrupted with high efficiency (~92%) in a single pass through a Constant Systems Cell Disruptor operated at 10 kpsi, releasing ~75% of the cellular iron. Magnetosomes were recovered in partially purified form from crude whole cell disruptates by rotor-stator high-gradient magnetic separation. Further purification/polishing was achieved by magnetically enhanced density separation in an aqueous micellar two-phase system (a new technique developed in this work as a low-cost alternative to sucrose gradient ultracentrifugation). The unoptimised 4-step process delivered highly purified magnetosomes (ca. 50 and 80-fold with respect to polyhydroxyalkanoate and protein) in >50% yield, with no evidence of crystal coat damage, acceptable reduction (~35%) in median magnetosome chain length, and magnetic properties (pot-bellied hysteresis loop, coercivity = 9.8 mT, ‘squareness’ = 0.32) expected of isolated magnetosome chains. Though demonstrated in batch mode, the platform displays potential for end-to-end continuous manufacture of future magnetosome-based products

Integrated system for temperature-controlled fast protein liquid chromatography comprising improved copolymer modified beaded agarose adsorbents and a travelling cooling zone reactor arrangement

An integrated approach to temperature-controlled chromatography, involving copolymer modified agarose adsorbents and a novel travelling cooling zone reactor (TCZR) arrangement, is described. Sepharose CL6B was transformed into a thermoresponsive cation exchange adsorbent (thermoCEX) in four synthetic steps: (i) epichlorohydrin activation; (ii) amine capping; (iii) 4,4′-azobis(4-cyanovaleric acid) immobilization; and ‘graft from’ polymerization of poly(N-isopropylacrylamide-co-N-tert-butylacrylamide-co-acrylic acid-co- N,N′-methylenebisacrylamide). FT-IR, 1H NMR, gravimetry and chemical assays allowed precise determination of the adsorbent’s copolymer composition and loading, and identified the initial epoxy activation step as a critical determinant of ‘on-support’ copolymer loading, and in turn, protein binding performance. In batch binding studies with lactoferrin, thermoCEX’s binding affinity and maximum adsorption capacity rose smoothly with temperature increase from 20 to 50 ºC. In temperature shifting chromatography experiments employing thermoCEX in thermally-jacketed columns, 44 – 51% of the lactoferrin adsorbed at 42 ºC could be desorbed under binding conditions by cooling the column to 22 ºC, but the elution peaks exhibited strong tailing. To more fully exploit the potential of thermoresponsive chromatography adsorbents, a new column arrangement, the TCZR, was developed. In TCZR chromatography, a narrow discrete cooling zone (special assembly of copper blocks and Peltier elements) is moved along a bespoke fixed-bed separation columnfilled with stationary phase. In tests with thermoCEX, it was possible to recover 65% of the lactoferrin bound at 35 ºC using 8 successive movements of the cooling zone at a velocity of 0.1 mm/s; over half of the recovered protein was eluted in the first peak in more concentrated form than in the feed. Intra-particle diffusion of desorbed protein out of the support pores, and the ratio between the velocities of the cooling zone and mobile phase were identified as the main parameters affecting TCZR performance. In contrast to conventional systems, which rely on cooling the 3 whole column to effect elution and permit only batch-wise operation, TCZR chromatography generates sharp concentrated elution peaks without tailing effects and appears ideally suited for continuous operation

Integrated system for temperature-controlled fast protein liquid chromatography. II. Optimized adsorbents and ‘single column continuous operation’

Continued advance of a new temperature-controlled chromatography system, comprising a column filled with thermoresponsive stationary phase and a travelling cooling zone reactor (TCZR), is described. Nine copolymer grafted thermoresponsive cation exchangers (thermoCEX) with different balances of thermoresponsive (N-isopropylacrylamide), hydrophobic (N-tert-butylacrylamide) and negatively charged (acrylic acid) units were fashioned from three cross-linked agarose media differing in particle size and pore dimensions. Marked differences in grafted copolymer composition on finished supports were sourced to base matrix hydrophobicity. In batch binding tests with lactoferrin, maximum binding capacity (q max) increased strongly as a function of charge introduced, but became increasingly independent of temperature, as the ability of the tethered copolymer networks to switch between extended and collapsed states was lost. ThermoCEX formed from Sepharose CL-6B (A2), Superose 6 Prep Grade (B2) and Superose 12 Prep Grade (C1) under identical conditions displayed the best combination of thermoresponsiveness (q max,50°C/q max,10°C ratios of 3.3, 2.2 and 2.8 for supports 'A2', 'B2' and 'C1' respectively) and lactoferrin binding capacity (q max,50°C ~56, 29 and 45mg/g for supports 'A2', 'B2' and 'C1' respectively), and were selected for TCZR chromatography. With the cooling zone in its parked position, thermoCEX filled columns were saturated with lactoferrin at a binding temperature of 35°C, washed with equilibration buffer, before initiating the first of 8 or 12 consecutive movements of the cooling zone along the column at 0.1mm/s. A reduction in particle diameter (A2→B2) enhanced lactoferrin desorption, while one in pore diameter (B2→C1) had the opposite effect. In subsequent TCZR experiments conducted with thermoCEX 'B2' columns continuously fed with lactoferrin or 'lactoferrin+bovine serum albumin' whilst simultaneously moving the cooling zone, lactoferrin was intermittently concentrated at regular intervals within the exiting flow as sharp uniformly sized peaks. Halving the lactoferrin feed concentration to 0.5mg/mL, slowed acquisition of steady state, but increased the average peak concentration factor from 7.9 to 9.2. Finally, continuous TCZR mediated separation of lactoferrin from bovine serum albumin was successfully demonstrated. While the latter's presence did not affect the time to reach steady state, the average lactoferrin mass per peak and concentration factor both fell (respectively from 30.7 to 21.4mg and 7.9 to 6.3), and lactoferrin loss in the flowthrough between elution peaks increased (from 2.6 to 12.2mg). Fouling of the thermoCEX matrix by lipids conveyed into the feed by serum albumin is tentatively proposed as responsible for the observed drops in lactoferrin binding and recovery

Empirical Phi-Discrepancies and Quasi-Empirical Likelihood: Exponential Bounds

We review some recent extensions of the so-called generalized empirical likelihood method, when the Kullback distance is replaced by some general convex divergence. We propose to use, instead of empirical likelihood, some regularized form or quasi-empirical likelihood method, corresponding to a convex combination of Kullback and χ2 discrepancies. We show that for some adequate choice of the weight in this combination, the corresponding quasi-empirical likelihood is Bartlett-correctable. We also establish some non-asymptotic exponential bounds for the confidence regions obtained by using this method. These bounds are derived via bounds for self-normalized sums in the multivariate case obtained in a previous work by the authors. We also show that this kind of results may be extended to process valued infinite dimensional parameters. In this case some known results about self-normalized processes may be used to control the behavior of generalized empirical likelihood