A histogram approach to the quality of fit in sedimentation velocity analyses

An automated interface for sedimentation velocity analysis in SEDFIT

Sedimentation velocity analytical ultracentrifugation (SV-AUC) is an indispensable tool for the study of particle size distributions in biopharmaceutical industry, for example, to characterize protein therapeutics and vaccine products. In particular, the diffusion-deconvoluted sedimentation coefficient distribution analysis, in the software SEDFIT, has found widespread applications due to its relatively high resolution and sensitivity. However, a lack of suitable software compatible with Good Manufacturing Practices (GMP) has hampered the use of SV-AUC in this regulatory environment. To address this, we have created an interface for SEDFIT so that it can serve as an automatically spawned module with controlled data input through command line parameters and output of key results in files. The interface can be integrated in custom GMP compatible software, and in scripts that provide documentation and meta-analyses for replicate or related samples, for example, to streamline analysis of large families of experimental data, such as binding isotherm analyses in the study of protein interactions. To test and demonstrate this approach we provide a MATLAB script mlSEDFIT.

SViMULATE: a computer program facilitating interactive, multi-mode simulation of analytical ultracentrifugation data

The ability to simulate sedimentation velocity (SV) analytical ultracentrifugation (AUC) experiments has proved to be a valuable tool for research planning, hypothesis testing, and pedagogy. Several options for SV data simulation exist, but they often lack interactivity and require up-front calculations on the part of the user. This work introduces SViMULATE, a program designed to make AUC experimental simulation quick, straightforward, and interactive. SViMULATE takes user-provided parameters and outputs simulated AUC data in a format suitable for subsequent analyses, if desired. The user is not burdened by the necessity to calculate hydrodynamic parameters for simulated macromolecules, as the program can compute these properties on the fly. It also frees the user of decisions regarding simulation stop time. SViMULATE features a graphical view of the species that are under simulation, and there is no limit on their number. Additionally, the program emulates data from different experimental modalities and data-acquisition systems, including the realistic simulation of noise for the absorbance optical system. The executable is available for immediate download.

An automated interface for sedimentation velocity analysis in SEDFIT

Sedimentation velocity analytical ultracentrifugation (SV-AUC) is an indispensable tool for the study of particle size distributions in biopharmaceutical industry, for example, to characterize protein therapeutics and vaccine products. In particular, the diffusion-deconvoluted sedimentation coefficient distribution analysis, in the software SEDFIT, has found widespread applications due to its relatively high resolution and sensitivity. However, a lack of available software compatible with Good Manufacturing Practices (GMP) has hampered the use of SV-AUC in this regulatory environment. To address this, we have created an interface for SEDFIT so that it can serve as an automatically spawned module with controlled data input through command line parameters and output of key results in files. The interface can be integrated in custom GMP compatible software, and in scripts that provide documentation and meta-analyses for replicate or related samples, for example, to streamline analysis of large families of experimental data, such as binding isotherm analyses in the study of protein interactions. To test and demonstrate this approach we provide a MATLAB script mlSEDFIT.

Boundary convection during velocity sedimentation in the Optima analytical ultracentrifuge

Analytical ultracentrifugation (AUC) provides the most widely applicable, precise, and accurate means for characterizing solution hydrodynamic and thermodynamic properties. While generally useful, boundary sedimentation velocity AUC (SV-AUC) analysis has become particularly important in assessing protein aggregation, fragmentation and conformational variants in the same solvents used during drug development and production. In early 2017 the only manufacturer of the analytical ultracentrifuge released its newest analytical ultracentrifuge, the Optima, to replace the aging second-generation XLA/I series ultracentrifuges. However, SV-AUC data from four Optima units used in the characterization of adeno-associated virus (AAV) have shown evidence of sample convection. Further investigation reveals this problem arises from the design of the temperature control system, which makes it prone to producing destabilizing temperature-induced density gradients that can lead to density inversions. The problem is intermittent and variable in severity within a given Optima unit and between Optima units. This convection appears to be associated mainly with low rotor speeds and dilute concentration of solvent components, i.e., AAV analysis conditions. Data features diagnostic for this problem and strategies for its elimination or minimization are provided.

Enhanced Sample Handling for Analytical Ultracentrifugation with 3D-Printed Centerpieces

The centerpiece of the sample cell assembly in analytical ultracentrifugation holds the sample solution between windows, sealed against high vacuum, and is shaped such that macromolecular migration in centrifugal fields exceeding 200 000g can proceed undisturbed by walls or convection while concentration profiles are imaged with optical detection systems aligned perpendicular to the plane of rotation. We have recently shown that 3D printing using various materials allows inexpensive and rapid manufacturing of centerpieces. In the present work, we expand this endeavor to examine the accuracy of the measured sedimentation process, as well as short-term durability of the centerpieces. We find that 3D-printed centerpieces can be used many times and can provide data equivalent in quality to commonly used commercial epoxy resin centerpieces. Furthermore, 3D printing enables novel designs adapted to particular experimental objectives because they offer unique opportunities, for example, to create well-defined curved surfaces, narrow channels, and embossed features. We present examples of centerpiece designs exploiting these capabilities for improved AUC experiments. This includes narrow sector centerpieces that substantially reduce the required sample volume while maintaining the standard optical path length; thin centerpieces with integrated window holders to provide very short optical pathlengths that reduce optical aberrations at high macromolecular concentrations; long-column centerpieces that increase the observable distance of macromolecular migration for higher-precision sedimentation coefficients; and three-sector centerpieces that allow doubling the number of samples in a single run while reducing the sample volumes. We find each of these designs allows unimpeded macromolecular sedimentation and can provide high-quality sedimentation data.

A survey of run-to-run control for batch processes

Run-to-run (R2R) control is widely used in semiconductor manufacturing systems to minimize the process drift, shift and variability. The R2R controller adjusts control actions or recipes in a supervisory manner after each batch. This paper provides a comprehensive literature review of R2R control methods for the batch process. First, the principles of major R2R controllers are introduced and analyzed, such as exponentially weighted moving average (EWMA), double exponentially weighted moving average (d-EWMA), model predictive control (MPC), optimizing adaptive quality controller (OAQC), artificial neural network (ANN). Besides, simulation examples with different R2R controllers are made to compare the robustness and adaptability. Then, several case studies concerning a chemical mechanical planarization (CMP) process, a multi-input and multi-output (MIMO) system of the furnace process control and the management of blood glucose (BG) are presented. Finally, the paper concludes with some recommendations and directions for the future research.

Returning Results: Let's Be Honest!

Biobank research has the potential to return results that could have beneficial and even life-saving consequences for participants. This possibility raises some important questions, not only about the ethical duty to return results within a research setting, but also about participants' right to refuse results and researchers' responsibility to respect that choice. This article argues in favor of adopting a return-of-results policy that limits participants' ability to refuse clinically relevant and actionable results. We state that biobanks should allow donors only if they are aware of and agree to this return policy. If they do not agree to this, they retain the option not to participate in the biobank research. The aim of this article is to discuss the practical and ethical reasons in favor of this return-of-result policy and, thus, to underline the importance of "honesty" in biobanking regulations.

Variable Field Analytical Ultracentrifugation: II. Gravitational Sweep Sedimentation Velocity

Sedimentation velocity (SV) analytical ultracentrifugation is a classical biophysical technique for the determination of the size-distribution of macromolecules, macromolecular complexes, and nanoparticles. SV has traditionally been carried out at a constant rotor speed, which limits the range of sedimentation coefficients that can be detected in a single experiment. Recently we have introduced methods to implement experiments with variable rotor speeds, in combination with variable field solutions to the Lamm equation, with the application to expedite the approach to sedimentation equilibrium. Here, we describe the use of variable-field sedimentation analysis to increase the size-range covered in SV experiments by ∼100-fold with a quasi-continuous increase of rotor speed during the experiment. Such a gravitational-sweep sedimentation approach has previously been shown to be very effective in the study of nanoparticles with large size ranges. In the past, diffusion processes were not accounted for, thereby posing a lower limit of particle sizes and limiting the accuracy of the size distribution. In this work, we combine variable field solutions to the Lamm equation with diffusion-deconvoluted sedimentation coefficient distributions c(s), which further extend the macromolecular size range that can be observed in a single SV experiment while maintaining accuracy and resolution. In this way, approximately five orders of magnitude of sedimentation coefficients, or eight orders of magnitude of particle mass, can be probed in a single experiment. This can be useful, for example, in the study of proteins forming large assemblies, as in fibrillation process or capsid self-assembly, in studies of the interaction between very dissimilar-sized macromolecular species, or in the study of broadly distributed nanoparticles.

Sedimentation coefficient distributions of large particles

The spatial and temporal evolution of concentration boundaries in sedimentation velocity analytical ultracentrifugation reports on the size distribution of particles with high hydrodynamic resolution. For large particles such as large protein complexes, fibrils, viral particles, or nanoparticles, sedimentation conditions usually allow migration from diffusion to be neglected relative to sedimentation. In this case, the shape of the sedimentation boundaries of polydisperse mixtures relates directly to the underlying size-distributions. Integral and derivative methods for calculating sedimentation coefficient distributions g*(s) of large particles from experimental boundary profiles have been developed previously, and are recapitulated here in a common theoretical framework. This leads to a previously unrecognized relationship between g*(s) and the time-derivative of concentration profiles. Of closed analytical form, it is analogous to the well-known Bridgman relationship for the radial derivative. It provides a quantitative description of the effect of substituting the time-derivative by scan differences with finite time intervals, which appears as a skewed box average of the true distribution. This helps to theoretically clarify the differences between results from time-derivative method and the approach of directly fitting the integral definition of g*(s) to the entirety of experimental boundary data.