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 E. 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 COMSOL code as well as master plots for estimation of sonication parameters (power input and pulse settings) is also presented.

Impact of ultrasound processing on alternative protein systems: Protein extraction, nutritional effects and associated challenges

“…(3) ). Power density is essential to control the cavitation effect as high power or high intensity when dissipated in a large volume of sample will not be effective in producing the cavitation effect as the US power density is decreased [73] . …”

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

“…The main sources of variability occur during the sample preparation. 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 . This leads to variation in the amount of surface defects and lengths, which in turn affects the fluorescence intensity and sensor response. − 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).…”

Enfuvirtide biosynthesis in thermostable chaperone-based fusion

“…In our practice, we used to record the specific presets for one specific sonicator. So, especially for reproducibility purposes and considering initial energy about 500 J/mL [23] , [24] , [25] , a new protocol was successfully tested with little lower energy applied, 300 J/mL. We should mention that energy efficiency of sonicator varies on model, probe, liquid volume and viscosity.…”