Search

John Ross Grace, one of the leading chemical engineers in Canada and an international figure in fluidization and fluid-particle systems, died in Vancouver on 26th May 2021, after a long fight with multiple system atrophy. At the same time, John and his colleagues at UBC developed a novel fluidized bed membrane reactor for hydrocarbon steam reforming for high-purity hydrogen production. As the Canada Research Chair in clean energy processes, John studied the combustion and gasification of coal and biomass in pilot fluidized bed reactors, and hydrocarbon steam reforming in pilot fluidized bed membrane reactors. [Extracted from the article]

Genotyping of the Kirsten Ras (KRAS) proto‐oncogene, particularly within its wild‐type (WT) codons G12 and G13, is used clinically to define courses of therapy for colorectal cancer (CRC). Stratification of CRC can be improved by genotyping BRAF in conjunction with KRAS, as missense (nonsynonymous) mutations (MTs) in BRAF V600 are frequently observed in MLH1‐deficient CRCs, and BRAF V600E‐positive tumours correlate with poor CRC patient outcomes. While next‐generation sequencing can be used to co‐genotype KRAS and BRAF, clinics could benefit from a faster, more cost‐effective assay of missense mutations in both KRAS and BRAF that unequivocally discriminates them from all known synonymous WT alleles. We previously reported a novel diagnostic technology that leverages the unique capabilities of droplet digital PCR (ddPCR) to achieve sensitive and quantitative detection of all known missense mutations in BRAF V600. Here, we report a ddPCR‐based method to co‐genotype KRAS G12/13 missense mutations and unequivocally differentiate them from all WT KRAS alleles. When combined with our test of BRAF status, the resulting inexpensive and rapid multiplex ddPCR assay accurately detects all known missense mutations in both KRAS G12/G13 and BRAF V600. The assay is applied to formalin‐fixed paraffin‐embedded tumour specimens from a cohort of 87 MLH1‐deficient CRC patients, and is shown to correctly identify BRAF V600 and KRAS G12/G13 missense mutations in each case. Two KRAS G12/13 mutation positive patients within the cohort are found to also carry a V600E missense mutation in BRAF. Pathological implications of this rarely observed co‐mutation are discussed. [ABSTRACT FROM AUTHOR]

Background: Achieving activity participation goals is a key factor in quality of life (QOL) for people with aphasia (PWA), but expressing participation goals can be difficult for many of them. Proxy reports by caregivers may not accurately reflect the interests and participation goals of PWA, and discrepancies in these goals between PWA and their caregivers may affect QOL, based on the assumption that caregivers' awareness of their loved ones' unique participation goals may be important to increasing PWA activity participation. Aims: To examine everyday activities valued by PWA using the Life Interests and Values (LIV) Cards; to measure congruence between PWA and their caregivers on life participation goals; and to measure how congruence of PWA–caregiver participation goals related to QOL. Methods & Procedures: A convenience sample of 25 PWA completed the LIV Card assessment and the Stroke Aphasia Quality of Life Scale—39 to assess participation goals and QOL. Participation goals were also evaluated with respect to age, time post‐onset and aphasia severity. A total of 12 caregivers were administered the LIV Cards to calculate agreement between PWA–proxy activity reports and the relationship between agreement and QOL. Outcomes & Results: PWA endorsed wanting to participate more in a wide range of activities, with common interests in walking/running, going to the beach and eating out, among others. PWA–caregiver activity agreement was fair to moderate with point‐to‐point agreement averaging 70%. However, no relationship between degree of congruence in PWA–proxy pairs and QOL was found. Conclusions & Implications: PWA have a variety of activity participation goals that can be integrated into intervention plans. Dependence on proxy respondents should be reduced as much as possible to support self‐determination for PWA. What this paper addsWhat is already known on the subjectAchieving activity participation goals is a key factor in QOL for PWA, but communicating about participation goals can be difficult for many of them. Because proxy reports by caregivers may not accurately reflect the interests and participation goals of PWA, this study examined how both PWA and their caregivers responded to an aphasia‐friendly assessment for determining participation goals, and then compared level of agreement about these goals to QOL. Because activity participation is known to be an important factor in QOL, the reason for investigating how agreement relates to QOL is that caregivers' awareness of their loved ones' unique participation goals likely facilitates increased participation by PWA in their ongoing desired activities. The relationship between PWA–caregiver agreement regarding participation goals and QOL in PWA had not yet been investigated before this study.What this paper adds to existing knowledgeThis study adds additional as well as confirmatory information to the existing literature about life participation goals of community‐dwelling individuals with chronic aphasia. Top activities endorsed by a group of 25 PWA are reported within four activity domains (home and community activities, creative and relaxing activities, physical activities, and social activities). Results indicated that agreement between PWA and their caregiver proxies on PWA's most desired activities was < 50%. However, the level of agreement between caregivers and proxies on participation goals was not significantly related to QOL in this sample.What are the potential or actual clinical implications of this work?PWA have a variety of participation goals that can be integrated into intervention plans to be carried out with clinicians, caregivers and family members. The use of proxy respondents when determining participation goals should be reduced as much as possible to support self‐determination for PWA. Use of the LIV Cards, a picture‐based sorting‐task assessment, reduces the need for proxy responders and guesswork about the specific participation goals of PWA. [ABSTRACT FROM AUTHOR]

Locked nucleic acids (LNAs) can greatly enhance duplex DNA stability, and are therefore creating opportunities to improve therapeutics, as well as PCR-based disease and pathogen diagnostics. Realizing the full potential of LNAs will require better understanding of their contributions to duplex stability, and the ability to predict their hydridization thermodynamics. Melting thermodynamics data for a large set of diverse duplexes containing LNAs in one or both strands are presented. Those data reveal that LNAs, when present on both strands, can stabilize a duplex not only through direct interaction with their base-pair partner, but also through nonlocal hyperstablization effects created by LNA:LNA base pairs and/or specific patterns of oppositely oriented LNA:DNA base pairs. The data are, therefore, used to extend a thermodynamic model previously developed in our lab to permit accurate prediction of melting temperatures for duplexes bearing LNA substitutions within both strands using a classic group-contribution approach. © 2015 American Institute of Chemical Engineers AIChE J, 61: 2711-2731, 2015 [ABSTRACT FROM AUTHOR]

ABSTRACT Current technologies for aptamer discovery typically leverage the systematic evolution of ligands by exponential enrichment (SELEX) concept by recursively panning semi-combinatorial ssDNA or RNA libraries against a molecular target. The expectation is that this iterative selection process will be sufficiently stringent to identify a candidate pool of specific high-affinity aptamers. However, failure of this process to yield promising aptamers is common, due in part to (i) limitations in library designs, (ii) retention of non-specific aptamers during screening rounds, (iii) excessive accumulation of amplification artifacts, and (iv) the use of screening criteria (binding affinity) that does not reflect therapeutic activity. We report a new selection platform, High-Fidelity (Hi-Fi) SELEX, that introduces fixed-region blocking elements to safeguard the functional diversity of the library. The chemistry of the target-display surface and the composition of the equilibration solvent are engineered to strongly inhibit non-specific retention of aptamers. Partition efficiencies approaching 106 are thereby realized. Retained members are amplified in Hi-Fi SELEX by digital PCR in a manner that ensures both elimination of amplification artifacts and stoichiometric conversion of amplicons into the single-stranded library required for the next selection round. Improvements to aptamer selections are first demonstrated using human α-thrombin as the target. Three clinical targets (human factors IXa, X, and D) are then subjected to Hi-Fi SELEX. For each, rapid enrichment of ssDNA aptamers offering an order-nM mean equilibrium dissociation constant ( Kd) is achieved within three selection rounds, as quantified by a new label-free qPCR assay reported here. Therapeutic candidates against factor D are identified. Biotechnol. Bioeng. 2015;112: 1506-1522. © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

ABSTRACT Standard libraries for systematic evolution of ligands by exponential enrichment (SELEX) typically utilize flanking regions that facilitate amplification of aptamers recovered from each selection round. Here, we show that these flanking sequences can bias the selection process, due in part to their ability to interfere with the fold or function of aptamers localized within the random region of the library sequence. We then address this problem by investigating the use of complementary oligonucleotides as a means to block aptamer interference by each flanking region. Isothermal titration calorimetry (ITC) studies are combined with fold predictions to both define the various interference mechanisms and assess the ability of added complementary oligonucleotides to ameliorate them. The proposed blocking strategy is thereby refined and then applied to standard library forms of benchmark aptamers against human α-thrombin, streptavidin, and vascular endothelial growth factor (VEGF). In each case, ITC data show that the new method effectively removes fixed-region mediated interference effects so that the natural binding affinity of the benchmark aptamer is completely restored. We further show that the binding affinities of properly functioning aptamers within a selection library are not affected by the blocking protocol, and that the method can be applied to various common library formats comprised of different flanking region sequences. Finally, we present a rapid and inexpensive qPCR-based method for determining the mean binding affinity of retained aptamer pools and use it to show that introduction of the pre-blocking method into the standard SELEX protocol results in retention of high-affinity aptamers that would otherwise be lost during the first round of selection. Significant enrichment of the available pool of high-affinity aptamers is thereby achieved in the first few rounds of selection. By eliminating single-strand (aptamer-like) structures within or involving the fixed regions, the technique is therefore shown to isolate aptamer sequence and function within the desired random region of the library members, and thereby provide a new selection method that is complementary to other available SELEX protocols. Biotechnol. Bioeng. 2014;111: 2265-2279. © 2014 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

ABSTRACT Membrane chromatography (MC) systems are finding increasing use in downstream processing trains for therapeutic proteins due to the unique mass-transfer characteristics they provide. As a result, there is increased need for model-based methods to scale-up MC units using data collected on a scaled-down unit. Here, a strategy is presented for MC unit scale-up using the zonal rate model (ZRM). The ZRM partitions an MC unit into virtual flow zones to account for deviations from ideal plug-flow behavior. To permit scale-up, it is first configured for the specific device geometry and flow profiles within the scaled-down unit so as to achieve decoupling of flow and binding related non-idealities. The ZRM is then configured for the preparative-scale unit, which typically utilizes markedly different flow manifolds and membrane architecture. Breakthrough is first analyzed in both units under non-binding conditions using an inexpensive tracer to independently determine unit geometry related parameters of the ZRM. Binding related parameters are then determined from breakthrough data on the scaled-down MC capsule to minimize sample requirements. Model-based scale-up may then be performed to predict band broadening and breakthrough curves on the preparative-scale unit. Here, the approach is shown to be valid when the Pall XT140 and XT5 capsules serve as the preparative and scaled-down units, respectively. In this case, scale-up is facilitated by our finding that the distribution of linear velocities through the membrane in the XT140 capsule is independent of the feed flow rate and the type of protein transmitted. Introduction of this finding into the ZRM permits quantitative predictions of breakthrough over a range of industrially relevant operating conditions. Biotechnol. Bioeng. 2014;111: 1587-1594. © 2014 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

ABSTRACT Experimental data are combined with classic theories describing electrolytes in solution and at surfaces to define the primary mechanisms influencing protein retention and elution during isoelectric chromatofocusing (ICF) of proteins and protein mixtures. Those fundamental findings are used to derive a new model to understand and predict elution times of proteins during ICF. The model uses a modified form of the steric mass action (SMA) isotherm to account for both ion exchange and isoelectric focusing contributions to protein partitioning. The dependence of partitioning on pH is accounted for through the characteristic charge parameter m of the SMA isotherm and the application of Gouy-Chapman theory to define the dependence of the equilibrium binding constant K bi on both m and ionic strength. Finally, the effects of changes in matrix surface pH on protein retention are quantified through a Donnan equilibrium type model. By accounting for isoelectric focusing, ion binding and exchange, and surface pH contributions to protein retention and elution, the model is shown to accurately capture the dependence of protein elution times on column operating conditions. Biotechnol. Biotechnol. Bioeng. 2014;111: 925-936. © 2014 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

ABSTRACT Isoelectric chromatofocusing (ICF), a mode of chromatography by which proteins are separated based on changes in their charge state with pH, is widely used at analytical scales and finding increasing interest in biologics manufacturing due to its exceptional resolving power. Here, a method is described for using simple monoprotic and diprotic buffers to create stable mobile phases for sample loading on a strong anion exchange column and for achieving an elution pH gradient of desired shape covering any pH range from pH 10.0 to 3. The buffers used are selected to satisfy cost constraints, and to permit facile detection of eluted biologics by UV spectroscopy and mass spectrometry. The method exploits a new model described here that combines multiple-chemical and adsorption-equilibria theory to enable in silico tailoring of elution pH profiles using mixtures of these simple buffers. It is shown to provide a versatile platform for optimizing and conducting ICF of protein mixtures on strong anion exchange media. Biotechnol. Bioeng. 2014;111: 552-564. © 2013 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The zonal rate model (ZRM) has previously been applied for analyzing the performance of axial flow membrane chromatography capsules by independently determining the impacts of flow and binding related non-idealities on measured breakthrough curves. In the present study, the ZRM is extended to radial flow configurations, which are commonly used at larger scales. The axial flow XT5 capsule and the radial flow XT140 capsule from Pall are rigorously analyzed under binding and non-binding conditions with bovine serum albumin (BSA) as test molecule. The binding data of this molecule is much better reproduced by the spreading model, which hypothesizes different binding orientations, than by the well-known Langmuir model. Moreover, a revised cleaning protocol with NaCl instead of NaOH and minimizing the storage time has been identified as most critical for quantitatively reproducing the measured breakthrough curves. The internal geometry of both capsules is visualized by magnetic resonance imaging (MRI). The flow in the external hold-up volumes of the XT140 capsule was found to be more homogeneous as in the previously studied XT5 capsule. An attempt for model-based scale-up was apparently impeded by irregular pleat structures in the used XT140 capsule, which might lead to local variations in the linear velocity through the membrane stack. However, the presented approach is universal and can be applied to different capsules. The ZRM is shown to potentially help save valuable material and time, as the experiments required for model calibration are much cheaper than the predicted large-scale experiment at binding conditions. Biotechnol. Bioeng. 2013; 110: 1129-1141. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The Zonal Rate Model (ZRM) has previously been shown to accurately account for contributions to elution band broadening, including external flow nonidealities and radial concentration gradients, in ion-exchange membrane (IEXM) chromatography systems operated under nonbinding conditions. Here, we extend the ZRM to analyze and model the behavior of retained proteins by introducing terms for intra-column mass transfer resistances and intrinsic binding kinetics. Breakthrough curve (BTC) data from a scaled-down anion-exchange membrane chromatography module using ovalbumin as a model protein were collected at flow rates ranging from 1.5 to 20 mL min−1. Through its careful accounting of transport nonidealities within and external to the membrane stack, the ZRM is shown to provide a useful framework for characterizing putative protein binding mechanisms and models, for predicting BTCs and complex elution behavior, including the common observation that the dynamic binding capacity can increase with linear velocity in IEXM systems, and for simulating and scaling separations using IEXM chromatography. Global fitting of model parameters is used to evaluate the performance of the Langmuir, bi-Langmuir, steric mass action (SMA), and spreading-type protein binding models in either correlating or fundamentally describing BTC data. When combined with the ZRM, the bi-Langmuir, and SMA models match the chromatography data, but require physically unrealistic regressed model parameters to do so. In contrast, for this system a spreading-type model is shown to accurately predict column performance while also providing a realistic fundamental explanation for observed trends, including an observed increase in dynamic binding capacity with flow rate. Biotechnol. Bioeng. 2012; 109:615-629. © 2011 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Copyright of Biotechnology Progress is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

A model describing elution-band profiles that combines multiple chemical equilibria theory with the nonideal equilibrium-dispersion equation for solute transport is used to predict and characterize the separation of l,d-dopa by chiral ligand-exchange chromatography (CLEC). Formation constants and stoichiometries for all equilibrium complexes formed in the interstitial volume and pore liquid are taken from standard thermodynamic databases and independent potentiometric titration experiments. Formation constants for complexes formed with the stationary phase ligand (N-octyl-3-octylthio-d-valine) are determined from potentiometric titration data for a water-soluble analogue of the ligand. This set of pure thermodynamic parameters is used to calculate the spatially discretized composition of each column volume element as a function of time. The model includes a temperature-dependent pure-component parameter, determined by regression to a single elution band for the pure component, that corrects for subtle effects associated with immobilizing the N-octyl-3-octylthio-d-valine ligand onto the stationary phase. The model is shown to accurately predict elution chromatograms and separation performance as a function of key column operating variables. The model is then used to better understand the connection between chemical equilibria within the system and changes in band profiles and band separation resulting from changes in column operating conditions. [ABSTRACT FROM AUTHOR]

The ability to translocate virulence proteins into host cells through a type III secretion apparatus (TTSS) is a hallmark of several Gram-negative pathogens including Shigella, Salmonella, Yersinia, Pseudomonas, and enteropathogenic Escherichia coli. In common with other types of bacterial secretion apparatus, the assembly of the TTSS complex requires the preceding formation of its integral outer membrane secretin ring component. We have determined at 1.5Åthe structure of MxiM28-142, the Shigella pilot protein that is essential for the assembly and membrane association of the Shigella secretin, MxiD. This represents the first atomic structure of a secretin pilot protein from the several bacterial secretion systems containing an orthologous secretin component. A deep hydrophobic cavity is observed in the novel‘cracked barrel’structure of MxiM, providing a specific binding domain for the acyl chains of bacterial lipids, a proposal that is supported by our various lipid/MxiM complex structures. Isothermal titration analysis shows that the C-terminal domain of the secretin, MxiD525-570, hinders lipid binding to MxiM. [ABSTRACT FROM AUTHOR]

The selective binding of the family 2a carbohydrate binding module (CBM2a) of xylanase 10A of the soil bacterium Cellulomonas fimi to a variety of cellulosic substrates is shown to provide a new, cost-effective affinity chromatography system for purification of recombinant protein. Genetic linkage of CBM2a to a target protein, in this case protein A from Staphylococcus aureus, results in a fusion protein that binds strongly to the particulate-cellulose resin Avicel PH101 and retains the biological activity of the fusion partner. Affinity purification of protein A-CBM2a from the supernatant of a recombinant E. coli JM101 culture results in a product purity of greater than 95% and a product concentration factor of 34 +/- 3. Measured column parameters are combined with one-dimensional equations governing continuity and intraparticle diffusion to predict product breakthrough curves with good accuracy over the range of realistic operating conditions. Peak spreading within the column is controlled by intraparticle diffusion for CBM2a and by a combination of film mass transfer and intraparticle diffusion for the larger protein A-CBM2a fusion protein.