Optimization of E. coli tip‐sonication for high‐yield cell‐free extract using finite element modeling

Abstract

Optimal tip sonication settings, namely tip position, input power, and pulse durations, are necessary for temperature sensitive procedures like preparation of viable cell extract. In this paper, the optimum tip immersion depth (20–30% height below the liquid surface) is estimated which ensures maximum mixing thereby enhancing thermal dissipation of local cavitation hotspots. A finite element (FE) heat transfer model is presented, validated experimentally with (R2 > 97%) and used to observe the effect of temperature rise on cell extract performance of Escherichia coli BL21 DE3 star strain and estimate the temperature threshold. Relative yields in the top 10% are observed for solution temperatures maintained below 32°C; this reduces below 50% relative yield at temperatures above 47°C. A generalized workflow for direct simulation using the CONSOL code as well as master plots for estimation of sonication parameters (power input and pulse settings) is also presented.

Single-Walled Carbon Nanotube Probes for the Characterization of Biofilm-Degrading Enzymes Demonstrated against Pseudomonas aeruginosa Extracellular Matrices

“…Despite careful attempts at weighing out materials and controlling process parameters, each batch of probes are prepared with slightly different amounts of SWCNTs and subjected to different levels of sonication power caused by different tip sonication positions. 68 This leads to variation in the amount of surface defects and lengths, which in turn affects the fluorescence intensity and sensor response. 69−71 These variations among the biofilm EPS-SWCNT probes can be improved by using automated sample preparation (robotic sonication) or other suspension techniques that have less variability (such as suspending a large batch with surfactants and then dialyzing to gently introduce EPS wrappings).…”

Novel methods to monitor the biodegradation of polylactic acid (PLA) by Amycolatopsis orientalis and Amycolatopsis thailandensis

“…This research proposes sonication treatment as the solution for both quantification problems. In microbiology, sonication is primarily used as an effective method for cell lysis and elimination of biofilms from surfaces ( Ganesan et al, 2015 ; Dudek et al, 2020 ; Ferdous et al, 2021 ). The ultrasound mechanism works by the propagation of sound waves from the sonicator along the medium, which induces a distinctive pressure difference.…”

Complex Dependence of Escherichia coli-based Cell-Free Expression on Sonication Energy During Lysis

“… 7 The extent of sonication can be controlled by, at fixed amplitude and burst time, monitoring the increase in energy input (e.g., in joules) while cycling between sonication bursts and cooling. The ideal energy input that results in maximal recombinant protein production can vary depending on the bacterial strain, the cell resuspension volume, the sonicator model, the immersion depth of the sonicator tip, 10 and even the operator’s technique. 4 However, once those variables are fixed, there seems to be a local optimum in energy that balances efficient membrane disruption with degradation of transcriptional and translational machineries, potentially due to heat shock.…”