Model-based analysis on the relationship of signal quality to real-time extraction of information in bioprocesses

Quality by design (QbD) is a current structured approach to design processes yielding a quality product. Knowledge and process understanding cannot be achieved without proper experimental data; hence requirements for measurement error and frequency of measurement of bioprocess variables have to be defined. In this contribution, a model-based approach is used to investigate impact factors on calculated rates to predict the obtainable information from real-time measurements (= signal quality). Measurement error, biological activity, and averaging window (= period of observation) were identified as biggest impact factors on signal quality. Moreover, signal quality has been set in context with a quantifiable measure using statistical error testing, which can be used as a benchmark for process analytics and exploitation of data. Results have been validated with data from an E. coli batch process. This approach is useful to get an idea which process dynamics can be observed with a given bioprocess setup and sampling strategy beforehand.     

Rate of loop formation in peptides: a simulation study

Experimental techniques with high temporal and spatial resolution extend our knowledge of how biological macromolecules self-organise and function. Here, we provide an illustration of the convergence between simulation and experiment made possible by techniques such as triplet-triplet energy transfer and fluorescence quenching with long-lifetime and fast-quenching fluorescent probes. These techniques have recently been used to determine the average time needed for two residues in a peptide or protein segment to form a contact. The timescale of this process is accessible to computer simulation, providing a microscopic interpretation of the data and yielding new insight into the disordered state of proteins. Conversely, such experimental data also provide a test of the validity of alternative choices for the molecular models used in simulations, indicating their possible deficiencies. We carried out simulations of peptides of various composition and length using several models. End-to-end contact formation rates and their dependence on peptide length agree with experimental estimates for some sequences and some force fields but not for others. The deviations are due to artefactual structuring of some peptides, which is not observed when an atomistic model for the solvation water is used. Simulations show that the observed experimental rates are compatible with considerably different distributions of the end-to-end distance; for realistic models, these are never Gaussian but indicative of a rugged energy landscape.     

Conserved central domains control the quaternary structure of type I and type II Hsp40 molecular chaperones

Heat shock protein (Hsp)40s play an essential role in protein metabolism by regulating the polypeptide binding and release cycle of Hsp70. The Hsp40 family is large, and specialized family members direct Hsp70 to perform highly specific tasks. Type I and Type II Hsp40s, such as yeast Ydj1 and Sis1, are homodimers that dictate functions of cytosolic Hsp70, but how they do so is unclear. Type I Hsp40s contain a conserved, centrally located cysteine-rich domain that is replaced by a glycine- and methionine-rich region in Type II Hsp40s, but the mechanism by which these unique domains influence Hsp40 structure and function is unknown. This is the case because high-resolution structures of full-length forms of these Hsp40s have not been solved. To fill this void, we built low-resolution models of the quaternary structure of Ydj1 and Sis1 with information obtained from biophysical measurements of protein shape, small-angle X-ray scattering, and ab initio protein modeling. Low-resolution models were also calculated for the chimeric Hsp40s YSY and SYS, in which the central domains of Ydj1 and Sis1 were exchanged. Similar to their human homologs, Ydj1 and Sis1 each has a unique shape with major structural differences apparently being the orientation of the J domains relative to the long axis of the dimers. Central domain swapping in YSY and SYS correlates with the switched ability of YSY and SYS to perform unique functions of Sis1 and Ydj1, respectively. Models for the mechanism by which the conserved cysteine-rich domain and glycine- and methionine-rich region confer structural and functional specificity to Type I and Type II Hsp40s are discussed.     

Case study and application of process analytical technology (PAT) towards bioprocessing: II. Use of ultra-performance liquid chromatography (UPLC) for making real-time pooling decisions for process chromatography

Process analytical technology (PAT) has been gaining a lot of momentum in the biopharmaceutical community due to the potential for continuous real-time quality assurance resulting in improved operational control and compliance. Two of the key goals that have been outlined for PAT are "variability is managed by the process" and "product quality attributes can be accurately and reliably predicted over the design space established for materials used, process parameters, manufacturing, environmental, and other conditions". Recently, we have been examining the feasibility of applying different analytical tools for designing PAT applications for bioprocessing. We have previously shown that a commercially available online high performance liquid chromatography (HPLC) system can be used for analysis that can facilitate real-time decisions for column pooling based on product quality attributes (Rathore et al., 2008). In this article we test the feasibility of using a commercially available ultra- performance liquid chromatography (UPLC) system for real-time pooling of process chromatography columns. It is demonstrated that the UPLC system offers a feasible approach and meets the requirements of a PAT application. While the application presented here is of a reversed phase assay, the approach and the hardware can be easily applied to other modes of liquid chromatography.     

On-line near infrared monitoring of glycerol-boosted anaerobic digestion processes: evaluation of process analytical technologies

A study of NIR as a tool for process monitoring of thermophilic anaerobic digestion boosted by glycerol has been carried out, aiming at developing simple and robust Process Analytical Technology modalities for on-line surveillance in full scale biogas plants. Three 5 L laboratory fermenters equipped with on-line NIR sensor and special sampling stations were used as a basis for chemometric multivariate calibration. NIR characterisation using Transflexive Embedded Near Infra-Red Sensor (TENIRS) equipment integrated into an external recurrent loop on the fermentation reactors, allows for representative sampling, of the highly heterogeneous fermentation bio slurries. Glycerol is an important by-product from the increasing European bio-diesel production. Glycerol addition can boost biogas yields, if not exceeding a limiting 5-7 g L(-1) concentration inside the fermenter-further increase can cause strong imbalance in the anaerobic digestion process. A secondary objective was to evaluate the effect of addition of glycerol, in a spiking experiment which introduced increasing organic overloading as monitored by volatile fatty acids (VFA) levels. High correlation between on-line NIR determinations of glycerol and VFA contents has been documented. Chemometric regression models (PLS) between glycerol and NIR spectra needed no outlier removals and only one PLS-component was required. Test set validation resulted in excellent measures of prediction performance, precision: r(2) = 0.96 and accuracy = 1.04, slope of predicted versus reference fitting. Similar prediction statistics for acetic acid, iso-butanoic acid and total VFA proves that process NIR spectroscopy is able to quantify all pertinent levels of both volatile fatty acids and glycerol.     

Social learning and life skills training for hatchery reared fish

With the stress placed on our natural resources, many fisheries increasingly rely on restocking from hatchery-reared sources in an attempt to maintain commercially viable populations. However, the mortality rates of hatchery-reared fishes during the period directly following release are very high. The successful development of restocking programs is consequently dependent upon production and release strategies that lead to improved migratory, antipredator and feeding behaviour in hatchery fish. While relevant individual experience prior to release might improve performance, social learning potentially provides a process whereby fish can acquire locally adaptive behaviour rapidly and efficiently. It is now well over a decade since Suboski & Templeton (1989) raised the possibility of using social learning processes to improve the post-release survival of hatchery-reared fishes. This period has witnessed considerable progress in the understanding of how social learning operates in fish populations. We review new methods and recent findings that suggest how social learning protocols could realistically be applied on a large scale to enhance the viability of hatchery fish prior to their release into the wild. We also suggest a practical pre-release training protocol that may be applied at the hatchery level.     

Effect of Calcium Ions on Hydrodynamic Properties of Pentameric and Decameric C-Reactive Protein in Solution

The molecular mass and sedimentation coefficient of native C-reactive protein in solution were determined by analytical ultracentrifugation in the presence and absence of calcium ions. Pentameric C-reactive protein was shown to be the major macroscopic form of this protein in solution. The removal of calcium ions from solution caused decompaction of the protein accompanied by changes in its hydrodynamic parameters. The sedimentation coefficient s ⁰ _20,w of pentameric C-reactive protein in solution containing 2 mM Ca²⁺ (6.6S) exceeded that for C-reactive protein in solution containing 2 mM EDTA (6.4S). Analysis of average molecular masses M _w and M _z obtained from sedimentation data demonstrated that the solution of highly purified protein was not homogeneous. As shown by intermolecular crosslinking, the solution also contained the 241-kDa decamer of C-reactive protein (9.5S) as a separate macroscopic form, whose share hardly reached 10% in the presence of 2 mM Ca²⁺ and increased after removal of calcium ions. The decamers were shown to result from intermolecular association of the pentamers.     

The Art of Sorting: Using Venn Diagrams to Learn Science Process Skills

In this article, the author describes activities that have been proven to teach young learners to sort and classify objects that contain more than one attribute. The activities require that students employ the use of sorting hoops and attribute blocks to create Venn diagrams, the assembly of which requires practice. The author also describes crosscurricular uses of these learning tools.