Full Pre-Steady-State Kinetic Analysis of Single Nucleotide Incorporation by DNA Polymerases

By measuring a DNA polymerase incorporation reaction on a very short time scale (5 ms to 10 s) and with a high enzyme concentration, the isolated event of a single nucleotide incorporation can be analyzed. Practically, this is done using a quench-flow instrument, which allows the rapid mixing of the enzyme-primer/template with the nucleotide substrate, after which the reaction is quenched and analyzed. We describe how to titrate the enzyme active site, how to determine, via a scouting experiment, the rate-limiting step in the polymerization reaction, and how to measure the apparent k_pol , K_d(DNA) , and K_d(N) using burst or single-turnover experiments. We include equations for the calculation of the processivity of the polymerase, its nucleotide incorporation specificity and preference, and the activation energy difference for the incorporation of an incorrect nucleotide. Data analysis is discussed, as this is an essential part of accurate data generation in kinetic analyses. © 2019 by John Wiley & Sons, Inc.

Kinetic analysis of N-alkylaryl carboxamide hexitol nucleotides as substrates for evolved polymerases

Six 1′,5′-anhydrohexitol uridine triphosphates were synthesized with aromatic substitutions appended via a carboxamide linker to the 5-position of their bases. An improved method for obtaining such 5-substituted hexitol nucleosides and nucleotides is described. The incorporation profile of the nucleotide analogues into a DNA duplex overhang using recently evolved XNA polymerases is compared. Long, mixed HNA sequences featuring the base modifications are generated. The apparent binding affinity of four of the nucleotides to the enzyme, the rate of the chemical step and of product release, plus the specificity constant for the incorporation of these modified nucleotides into a DNA duplex overhang using the HNA polymerase T6G12_I521L are determined via pre-steady-state kinetics. HNA polymers displaying aromatic functional groups could have significant impact on the isolation of stable and high-affinity binders and catalysts, or on the design of nanomaterials.

A fungal biofilm reactor based on metal structured packing improves the quality of a Gla::GFP fusion protein produced by Aspergillus oryzae

Fungal biofilm is known to promote the excretion of secondary metabolites in accordance with solid-state-related physiological mechanisms. This work is based on the comparative analysis of classical submerged fermentation with a fungal biofilm reactor for the production of a Gla::green fluorescent protein (GFP) fusion protein by Aspergillus oryzae. The biofilm reactor comprises a metal structured packing allowing the attachment of the fungal biomass. Since the production of the target protein is under the control of the promoter glaB, specifically induced in solid-state fermentation, the biofilm mode of culture is expected to enhance the global productivity. Although production of the target protein was enhanced by using the biofilm mode of culture, we also found that fusion protein production is also significant when the submerged mode of culture is used. This result is related to high shear stress leading to biomass autolysis and leakage of intracellular fusion protein into the extracellular medium. Moreover, 2-D gel electrophoresis highlights the preservation of fusion protein integrity produced in biofilm conditions. Two fungal biofilm reactor designs were then investigated further, i.e. with full immersion of the packing or with medium recirculation on the packing, and the scale-up potentialities were evaluated. In this context, it has been shown that full immersion of the metal packing in the liquid medium during cultivation allows for a uniform colonization of the packing by the fungal biomass and leads to a better quality of the fusion protein.

A non-linear homogeneous model for bone-like materials under compressive load

Finite element (FE) models accurately compute the mechanical response of bone and bone-like materials when the models include their detailed microstructure. In order to simulate non-linear behavior, which currently is only feasible at the expense of extremely high computational costs, coarser models can be used if the local morphology has been linked to the apparent mechanical behavior. The aim of this paper is to implement and validate such a constitutive law. This law is able to capture the non-linear structural behavior of bone-like materials through the use of fabric tensors. It also allows for irreversible strains using an elastoplastic material model incorporating hardening. These features are expressed in a constitutive law based on the anisotropic continuum damage theory coupled with isotropic elastoplasticity in a finite strain framework. This material model was implemented into metafor (LTAS-MNNL, University of Liège, Belgium), a non-linear FE software. The implementation was validated against experimental data of cylindrical samples subjected to compression. Three materials with bone-like microstructure were tested: aluminum foams of variable density (ERG, Oakland, CA, USA), polylactic acid foam (CERM, University of Liège, Liège, Belgium), and cancellous bone tissue of a deer antler (Faculty of Veterinary Medicine, University of Liège, Liège, Belgium).

Influence of back mixing on the convective drying of residual sludges in a fixed bed

The influence of a backmixing operation on the convective belt drying of two wastewater sludges was studied. The expansion of the sludge extrudates bed due to increasing additions of dry product was quantified by using X-ray tomography. This non-invasive technique was used to determine the bed porosity and the total exchange area available for heat and mass transfers, for increasing levels of backmixing. For a same drying flux, the expansion of the drying bed leads to higher drying rates, allowing a reduction of the total drying time. In this context, rheological properties of the sludges are key properties.