Purification of plasmid DNA for use in human gene therapy

Two key issues defined the focus of this research in manufacturing plasmid DNA for use In human gene therapy. First, the processing of E.coli bacterial cells to effect the separation of therapeutic plasmid DNA from cellular debris and adventitious material. Second, the affinity purification of the plasmid DNA in a Simple one-stage process. The need arises when considering the concerns that have been recently voiced by the FDA concerning the scalability and reproducibility of the current manufacturing processes in meeting the quality criteria of purity, potency, efficacy, and safety for a recombinant drug substance for use in humans. To develop a preliminary purification procedure, an EFD cross-flow micro-filtration module was assessed for its ability to effect the 20-fold concentration, 6-time diafiltration, and final clarification of the plasmid DNA from the subsequent cell lysate that is derived from a 1 liter E.coli bacterial cell culture. Historically, the employment of cross-flow filtration modules within procedures for harvesting cells from bacterial cultures have failed to reach the required standards dictated by existing continuous centrifuge technologies, frequently resulting in the rapid blinding of the membrane with bacterial cells that substantially reduces the permeate flux. By challenging the EFD module, containing six helical wound tubular membranes promoting centrifugal instabilities known as Dean vortices, with distilled water between the Dean number's of 187Dn and 818Dn,and the transmembrane pressures (TMP) of 0 to 5 psi. The data demonstrated that the fluid dynamics significantly influenced the permeation rate, displaying a maximum at 227Dn (312 Imh) and minimum at 818Dn (130 Imh) for a transmembrane pressure of 1 psi. Numerical studies indicated that the initial increase and subsequent decrease resulted from a competition between the centrifugal and viscous forces that create the Dean vortices. At Dean numbers between 187Dn and 227Dn , the forces combine constructively to increase the apparent strength and influence of the Dean vortices. However, as the Dean number in increases above 227 On the centrifugal force dominates the viscous forces, compressing the Dean vortices into the membrane walls and reducing their influence on the radial transmembrane pressure i.e. the permeate flux reduced. When investigating the action of the Dean vortices in controlling tile fouling rate of E.coli bacterial cells, it was demonstrated that the optimum cross-flow rate at which to effect the concentration of a bacterial cell culture was 579Dn and 3 psi TMP, processing in excess of 400 Imh for 20 minutes (i.e., concentrating a 1L culture to 50 ml in 10 minutes at an average of 450 Imh). The data demonstrated that there was a conflict between the Dean number at which the shear rate could control the cell fouling, and the Dean number at which tile optimum flux enhancement was found. Hence, the internal geometry of the EFD module was shown to sub-optimal for this application. At 579Dn and 3 psi TMP, the 6-fold diafiltration was shown to occupy 3.6 minutes of process time, processing at an average flux of 400 Imh. Again, at 579Dn and 3 psi TMP the clarification of the plasmid from tile resulting freeze-thaw cell lysate was achieved at 120 Iml1, passing 83% (2,5 mg) of the plasmid DNA (6,3 ng μ-1 10.8 mg of genomic DNA (∼23,00 Obp, 36 ng μ-1 ), and 7.2 mg of cellular proteins (5-100 kDa, 21.4 ngμ-1 ) into the post-EFD process stream. Hence the EFD module was shown to be effective, achieving the desired objectives in approximately 25 minutes. On the basis of its ability to intercalate into low molecular weight dsDNA present in dilute cell lysates, and be electrophoresed through agarose, the fluorophore PicoGreen was selected for the development of a suitable dsDNA assay. It was assesseel for its accuracy, and reliability, In determining the concentration and identity of DNA present in samples that were eleclrophoresed through agarose gels. The signal emitted by intercalated PicoGreen was shown to be constant and linear, and that the mobility of the PicaGreen-DNA complex was not affected by the intercalation. Concerning the secondary purification procedure, various anion-exchange membranes were assessed for their ability to capture plasmid DNA from the post-EFD process stream. For a commercially available Sartorius Sartobind Q15 membrane, the reduction in the equilibriumbinding capacity for  ctDNA in buffer of increasing ionic demonstrated that DNA was being.adsorbed by electrostatic  interactions only. However, the problems associated with fluid distribution across the membrane demonstrated that the membrane housing was the predominant cause of the .erratic breakthrough curves. Consequently, this would need to be rectified before such a membrane could be integrated into the current system, or indeed be scaled beyond laboratory scale. However, when challenged with the process material, the data showed that considerable quantities of protein (1150 μg) were adsorbed preferentially to the plasmid DNA (44 μg). This was also shown for derived Pall Gelman UltraBind US450 membranes that had been functionalised by varying molecular weight poly-L~lysine and polyethyleneimine ligands. Hence the anion-exchange membranes were shown to be ineffective in capturing plasmid DNA from the process stream. Finally, work was performed to integrate a sequence-specific DNA·binding protein into a single-stage DNA chromatography, isolating plasmid DNA from E.coli cells whilst minimising the contamination from genomic DNA and cellular protein. Preliminary work demonstrated that the fusion protein was capable of isolating pUC19 DNA into which the recognition sequence for the fusion-protein had been inserted (pTS DNA) when in the presence of the conditioned process material. Althougth the pTS recognition sequence differs from native pUC19 sequences by only 2 bp, the fusion protein was shown to act as a highly selective affinity ligand for pTS DNA alone. Subsequently, the scale of the process was scaled 25-fold and positioned directly following the EFD system. In conclusion, the integration of the EFD micro-filtration system and zinc-finger affinity purification technique resulted in the capture of approximately 1 mg of plasmid DNA was purified from 1L of E.coli  culture in a simple two stage process, resulting in the complete removal of genomic DNA and 96.7% of cellular protein in less than 1 hour of process time.

Pattern generation by dissipative parametric instability

Nonlinear instabilities are responsible for spontaneous pattern formation in a vast number of natural and engineered systems, ranging from biology to galaxy buildup. We propose a new instability mechanism leading to pattern formation in spatially extended nonlinear systems, which is based on a periodic antiphase modulation of spectrally dependent losses arranged in a zigzag way: an effective filtering is imposed at symmetrically located wave numbers k and -k in alternating order. The properties of the dissipative parametric instability differ from the features of both key classical concepts of modulation instabilities, i.e., the Benjamin-Feir instability and the Faraday instabiltyity. We demonstrate how the dissipative parametric instability can lead to the formation of stable patterns in one- and two-dimensional systems. The proposed instability mechanism is generic and can naturally occur or can be implemented in various physical systems.

Techniques for determining bias and stability in satellite altimeters

The case for monitoring large-scale sea level variability is established in the context of the estimation of the extent of anthropogenic climate change. Satellite altimeters are identified as having the potential to monitor this change with high resolution and accuracy. Possible sources of systematic errors and instabilities in these instruments which would be hurdles to the most accurate monitoring of such ocean signals are examined. Techniques for employing tide gauges to combat such inaccuracies are proposed and developed. The tide gauge at Newhaven in Sussex is used in conjunction with the nearby satellite laser ranger and high-resolution ocean models to estimate the absolute bias of the TOPEX, Poseidon, ERS 1 and ERS 2 altimeters. The theory which underlies the augmentation of altimeter measurements with tide gauge data is developed. In order to apply this, the tide gauges of the World Ocean Circulation Experiment are assessed and their suitability for altimeter calibration is determined. A reliable subset of these gauges is derived. A method of intra-altimeter calibration is developed using these tide gauges to remove the effect of variability over long time scales. In this way the long-term instability in the TOPEX range measurement is inferred and the drift arising from the on-board ultra stable oscillator is thus detected. An extension to this work develops a method for inter-altimeter calibration, allowing the systematic differences between unconnected altimeters to be measured. This is applied to the TOPEX and ERS 1 altimeters.

Unrepeatered field transmission of 2 Tbit/s multi-banded coherent WDM over 124 km of installed SMF

In this paper we report field transmission of a 2Tbit/s multi-banded Coherent WDM signal over BT Ireland's installed SMF, using EDFA amplification only, with mixed Ethernet (with FEC) and PRBS payloads. To the best of our knowledge, the results obtained represent the highest total capacity transmitted over installed SMF with orthogonal subcarriers. BERs below 10(-5) and no frame-loss were recorded for all 49 subcarriers. Extended BER measurements over several hours showed fluctuations that can be attributed to PMD and to dynamic effects associated with clock instabilities.

Comparison between femtosecond laser and fusion-arc inscribed long period gratings in photonic crystal fibre

The use of high intensity femtosecond laser sources for inscribing fibre gratings has attained significant interest. The principal advantage of high-energy pulses is their ability for grating inscription in any material type without preprocessing or special core doping. In the field of fibre optical sensing LPGs written in photonic crystal fibre have a distinct advantage of low temperature sensitivity over gratings written in conventional fibre and thus minimal temperature cross-sensitivity. Previous studies have indicated that LPGs written by a point-by-point inscription scheme using a low repetition femtosecond laser exhibit post-fabrication evolution leading to temporal instabilities at room temperatures with respect to spectral location, strength and birefringence of the attenuation bands. These spectral instabilities of LPGs are studied in photonic crystal fibres (endlessly single mode microstructure fibre) to moderately high temperatures 100°C to 200°C and their performance compared to fusion-arc fabricated LPG. Initial results suggest that the fusion-arc fabricated LPG demonstrate less spectral instability for a given constant and moderate temperature, and are similar to the results obtained when inscribed in a standard single mode fibre.

Coherence and anticoherence resonance in high-concentration erbium-doped fiber laser

We report an experimental study of low-frequency (~10 kHz) self-pulsing of the output intensity in a high- concentration erbium-doped fiber laser. We suggest that the fast intensity fluctuations caused by multimode and polarization instabilities play the role of an external noise source, leading to low-frequency auto-oscillations through a coherence resonance scenario.

Mode-locked semiconductor lasers with optical injection

We perform characterization of the pulse shape and noise properties of quantum dot passively mode-locked lasers (PMLLs). We propose a novel method to determine the RF linewidth and timing jitter, applicable to high repetition rate PMLLs, through the dependence of modal linewidth on the mode number. Complex electric field measurements show asymmetric pulses with parabolic phase close to threshold, with the appearance of waveform instabilities at higher currents. We demonstrate that the waveform instabilities can be overcome through optical injection-locking to the continues wave (CW) master laser, leading to time-bandwidth product (TBP) improvement, spectral narrowing, and spectral tunability. We discuss the benefits of single- and dual-tone master sources and demonstrate that dual-tone optical injection can additionally improve the noise properties of the slave laser with RF linewidth reduction below instrument limits (1 kHz) and integrated timing jitter values below 300 fs. Dual-tone injection allowed slave laser repetition rate control over a 25 MHz range with reduction of all modal optical linewidths to the master source linewidth, demonstrating phase-locking of all slave modes and coherence improvement.

Mode-locked semiconductor lasers with optical injection

We perform characterization of the pulse shape and noise properties of quantum dot passively mode-locked lasers (PMLLs). We propose a novel method to determine the RF linewidth and timing jitter, applicable to high repetition rate PMLLs, through the dependence of modal linewidth on the mode number. Complex electric field measurements show asymmetric pulses with parabolic phase close to threshold, with the appearance of waveform instabilities at higher currents. We demonstrate that the waveform instabilities can be overcome through optical injection-locking to the continues wave (CW) master laser, leading to time-bandwidth product (TBP) improvement, spectral narrowing, and spectral tunability. We discuss the benefits of single- and dual-tone master sources and demonstrate that dual-tone optical injection can additionally improve the noise properties of the slave laser with RF linewidth reduction below instrument limits (1 kHz) and integrated timing jitter values below 300 fs. Dual-tone injection allowed slave laser repetition rate control over a 25 MHz range with reduction of all modal optical linewidths to the master source linewidth, demonstrating phase-locking of all slave modes and coherence improvement.

Cross-correlation-aided transport in stochastically driven accretion flows

The origin of linear instability resulting in rotating sheared accretion flows has remained a controversial subject for a long time. While some explanations of such non-normal transient growth of disturbances in the Rayleigh stable limit were available for magnetized accretion flows, similar instabilities in the absence of magnetic perturbations remained unexplained. This dichotomy was resolved in two recent publications by Chattopadhyay and co-workers [Mukhopadhyay and Chattopadhyay, J. Phys. A 46, 035501 (2013)1751-811310.1088/1751-8113/46/3/035501; Nath, Phys. Rev. E 88, 013010 (2013)PLEEE81539-375510.1103/PhysRevE.88.013010] where it was shown that such instabilities, especially for nonmagnetized accretion flows, were introduced through interaction of the inherent stochastic noise in the system (even a "cold" accretion flow at 3000 K is too "hot" in the statistical parlance and is capable of inducing strong thermal modes) with the underlying Taylor-Couette flow profiles. Both studies, however, excluded the additional energy influx (or efflux) that could result from nonzero cross correlation of a noise perturbing the velocity flow, say, with the noise that is driving the vorticity flow (or equivalently the magnetic field and magnetic vorticity flow dynamics). Through the introduction of such a time symmetry violating effect, in this article we show that nonzero noise cross correlations essentially renormalize the strength of temporal correlations. Apart from an overall boost in the energy rate (both for spatial and temporal correlations, and hence in the ensemble averaged energy spectra), this results in mutual competition in growth rates of affected variables often resulting in suppression of oscillating Alfven waves at small times while leading to faster saturations at relatively longer time scales. The effects are seen to be more pronounced with magnetic field fluxes where the noise cross correlation magnifies the strength of the field concerned. Another remarkable feature noted specifically for the autocorrelation functions is the removal of energy degeneracy in the temporal profiles of fast growing non-normal modes leading to faster saturation with minimum oscillations. These results, including those presented in the previous two publications, now convincingly explain subcritical transition to turbulence in the linear limit for all possible situations that could now serve as the benchmark for nonlinear stability studies in Keplerian accretion disks.

Optimization of erbium-doped actively Q-switched fiber laser implemented in symmetric configuration

We report the results of an experimental study aimed at improving the performance of actively Q-switched fiber lasers. Unlike generic design schemes employing photonic crystal fibers, largemodal diameter fibers or double-clad fibers, we demonstrate a high-power, actively Q-switched laser based on standard com- munication erbium doped fibers with peak irradiance beyond the state-of-the-art at 3.1 GW/cm2 . The laser had 2.2 kW peak power, 15.5 ns pulse duration and 36.8 µJ pulse energy. We have also investigated the dynamics of pulse generation and have success- fully suppressed pulse instabilities caused by backscattered laser emission reaching the pump laser diodes.

The role of pinning and instability in a class of non-equilibrium growth models

We study the dynamics of a growing crystalline facet where the growth mechanism is controlled by the geometry of the local curvature. A continuum model, in (2+1) dimensions, is developed in analogy with the Kardar-Parisi-Zhang (KPZ) model is considered for the purpose. Following standard coarse graining procedures, it is shown that in the large time, long distance limit, the continuum model predicts a curvature independent KPZ phase, thereby suppressing all explicit effects of curvature and local pinning in the system, in the "perturbative" limit. A direct numerical integration of this growth equation, in 1+1 dimensions, supports this observation below a critical parametric range, above which generic instabilities, in the form of isolated pillared structures lead to deviations from standard scaling behaviour. Possibilities of controlling this instability by introducing statistically "irrelevant" (in the sense of renormalisation groups) higher ordered nonlinearities have also been discussed.

Dropout dynamics in pulsed quantum dot lasers due to mode jumping

We examine the response of a pulse pumped quantum dot laser both experimentally and numerically. As the maximum of the pump pulse comes closer to the excited-state threshold, the output pulse shape becomes unstable and leads to dropouts. We conjecture that these instabilities result from an increase of the linewidth enhancement factor α as the pump parameter comes close to the excitated state threshold. In order to analyze the dynamical mechanism of the dropout, we consider two cases for which the laser exhibits either a jump to a different single mode or a jump to fast intensity oscillations. The origin of these two instabilities is clarified by a combined analytical and numerical bifurcation diagram of the steady state intensity modes.

Failure to relaunch? The United States, nuclear North Korea, and the future of the six-party talks

During the past twenty years, Washington has oscillated between tentative engagement with Pyongyang under the Clinton administration and isolation and multilateralism under the Bush administration. With the Obama administration almost nearing its four-year tenure, the Six-Party Talks have stalled and North Korea's multiple attacks on the South in 2010 have created new instabilities. Why so little results despite promises of a radical departure away from the Axis of Evil rhetoric and hard-line politics? This paper suggests that the Obama administration has utilized approaches that no longer fit current circumstances and hence failed to create an original, coherent and effective foreign policy. © 2012 McFarland & Company, Inc.

Practical and cost-effective high-fidelity optical carrier dissemination using coherent communication techniques

We report a unidirectional frequency dissemination scheme for high-fidelity optical carriers deployable over telecommunication networks. For the first time, a 10 Gb/s Binary Phase Shift Keying (BPSK) signal from an ultra-narrow linewidth laser was transmitted through a field-installed optical fibre with round-trip length of 124 km between Cork City and town of Clonakilty, without inline optical amplification. At the receiver, using coherent communication techniques and optical injection-locking the carrier was recovered with noise suppression. The beat signal between the original carrier at the transmitter and recovered carrier at the receiver shows a linewidth of 2.8 kHz. Long term stability measurements revealed fractional instabilities (True Allan deviation) of 3.3 × 10-14 for 1 s averaging time, prior to phase noise cancellation.

Passive mode locking in erbium-doped fibre laser by carbon nanotubes

Passively mode locked fibre lasers have a variety of applications ranging from telecommunication to medical photonics. Carbon nanotubes (CNTs) have attracted recently a great deal of attention as a promising solution for saturable absorber elements required for laser mode locking (see e.g. [1-3] and references therein). CNTs can be used as a saturable absorber in passively mode locked fibre laser directly [1,2] or as a CNTs polymer composites [3]. An attractive feature of CNT-based solutions in fibre lasers is a possibility to maintain the compactness, robustness of all-fibre format and low cost through using all standard telecom compatible components. The two important technical challenges in such type of lasers are: (i) to achieve stable polarization properties of the generated radiation without using complex control elements, and, (ii) to avoid low frequency instabilities of the mode-locked pulse train. In this paper we report results of the experiments on mode-locked soliton fibre laser using the following standard components: 1m of highly doped erbium fibre (Liekki Er80-8/125) serves as the gain medium with nominal absorption of 80 dB/m at 1530 nm; a 976 nm laser diode providing up to 310mW power is used to pump the laser via a 980/1550 wavelength division multiplexing; an isolator is employed to ensure single direction oscillation; SMF-28 is used to create necessary amount of anomalous dispersion to form soliton pulse making the total cavity length around 7.83 m; the CNT-polyvinyl alcohol polymer saturable absorber sandwiched in the FC/PC connector is used as a mode-locker device (see [3] for details). © 2011 IEEE.