Methods for the Measurement of a Bacterial Enzyme Activity in Cell Lysates and Extracts

Screening of angiotensin converting enzyme inhibitors from natural products via origami microfluidic paper-based analytical devices with colorimetric detection

We report the screening of angiotensin converting enzyme (ACE) inhibitors on an origami microfluidic paper-based analytical device (μPAD) using colorimetric detection. The hydrolysis product reacts with ninhydrin, resulting in a purple color at the detection zones. Images of the μPADs are captured using a common cell phone and analyzed with Photoshop software. This platform allows six independent colorimetric reactions to take place simultaneously, and the IC50 values can be obtained in a single run within 22 min. The relative standard deviations of inhibition efficiencies are generally lower than 4.0 % (n = 5). The IC50 values of captopril and five products from natural plants were obtained and corresponded well with UV methods. The relative deviations between the two methods are within the range of -5 % to +5 %. This work is a proof-of-concept successfully demonstrating the use of μPADs technology to screen enzyme inhibitors from natural products.

dsRNase1 contribution to dsRNA degradation activity in the Sf9 cells conditioned medium

RNA interference (RNAi) is inefficient in lepidopteran insects, including Spodoptera frugiperda. RNase activity in the lumen and hemocoel is known to contribute to low RNAi efficiency in these insects. Conditioned medium from Sf9 cells developed from ovaries of S. frugiperda shows high dsRNA degradation activity. But the enzymes responsible for this activity have not been identified. The nuclease genes that are highly expressed in Sf9 cells, REase, RNaseT2, and dsRNase1, were identified. Knockdown of dsRNase1 in Sf9 cells resulted in a reduction of dsRNA degradation activity in the Sf9 cells conditioned medium. Knockdown of dsRNase1 also increased RNAi efficiency in Sf9 cells. The results from these studies identified a major player in dsRNA degradation activity in the Sf9 cells conditioned medium. We also describe an efficient system that can be used to identify other genes responsible for dsRNA degradation and RNAi efficiency in Sf9 cells.

Determination of online quenching efficiency for an automated cellular microfluidic metabolomic platform using mass spectrometry based ATP degradation analysis

As microfluidic cell culture progresses, the need for robust and reproducible intracellular analyses grows. In particular, intracellular metabolites are subject to perturbation and degradation during the lysing process. The reliability of intracellular metabolomic analysis in microfluidic devices depends on the preservation of metabolite integrity during sample preparation and storage. Described here is a novel automated microfluidic system exhibiting the necessary rapid cellular lysis and quenching of enzymatic activity. Quenching efficiency was assessed using a novel ratiometric MALDI-MS-based assay of exogenous isotopic adenosine triphosphate (ATP) hydrolysis to isotopic adenosine diphosphate (ADP) as a marker of metabolite degradation. The lysis system of the microfluidic device was enhanced using a Peltier cooler to chill the lysate and quench aberrant enzymatic activity. Parameter optimization (flow rate, collection time, and temperature control) improved the endogenous and exogenous ADP/ATP ratios by 44.9% and 39.8% respectively consistent with traditional quenching techniques. The effects of chilling/quenching on metabolism were evaluated resulting in over 500 significant features compared to non-chilled from untargeted capillary LC-MS metabolomic analyses. These include increased levels of tryptophan, histidine, and pyruvate as well as decreased levels in UDP-N-acetylglucosamine. The results illustrate the need for both rapid lysis and quenching in microfluidic cell culture platforms. Graphical abstract.

Optimization and comparative characterization of neuraminidase activities from Pseudomonas aeruginosa with Klebsiella pneumoniae, Hep-2 cell, sheep kidney and rat liver lysosome

BACKGROUND AND OBJECTIVES

The properties of neuraminidase produced by P. aeruginosa strain PAO1 during growth in a defined medium (BHI) was examined and compared with some neuraminidase features of K. pneumoniae in this investigation.

MATERIALS AND METHODS

The enzyme was isolated from concentrated culture supernatants of P. aeruginosa which was used in a sensitive fluorometric assay by using 2'-(4-methylumbelliferyl) α-D-N acetylneuraminic acid as substrate.

RESULTS

Neuraminidase production in P. aeruginosa PAO1 paralleled bacterial growth in defined medium (BHI) and was maximal in the late logarithmic phase of growth but decreased during the stationary phase, probably owing to protease production or thermal instability. Highest production of P. aeruginosa PAO1 neuraminidase was in BHI culture media. The neuraminidase of P. aeruginosa PAO1 possessed an optimum temperature of activity at 56°C and the activity was maximal at pH 5. Heating the enzyme to 56°C for 45 min., in the presence of bovine serum albumin destroyed 33.1% of it's activity and addition of Ca(+2), EDTA and NANA also decreased activity markedly.

CONCLUSION

The results revealed that the highest specific activity is for p. aeruginosa PAO1.

High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis of base-specific cleavage products is an efficient, highly accurate tool for the detection of single base sequence variations. We describe the first application of this comparative sequencing strategy for automated high-throughput mutation detection in microbial genomes. The method was applied to identify DNA sequence changes that occurred in Escherichia coli K-12 MG1655 during laboratory adaptive evolution to new optimal growth phenotypes. Experiments were based on a genome-scale in silico model of E. coli metabolism and growth. This model computes several phenotypic functions and predicts optimal growth rates. To identify mutations underlying a 40-d adaptive laboratory evolution on glycerol, we resequenced 4.4% of the E. coli-K12 MG1655 genome in several clones picked at the end of the evolutionary process. The 1.54-Mb screen was completed in 13.5 h. This resequencing study is the largest reported by MALDI-TOF mass spectrometry to date. Ten mutations in 40 clones and three deviations from the reference sequence were detected. Mutations were predominantly found within the glycerol kinase gene. Functional characterization of the most prominent mutation shows its metabolic impact on the process of adaptive evolution. All sequence changes were independently confirmed by genotyping and Sanger-sequencing. We demonstrate that comparative sequencing by base-specific cleavage and MALDI-TOF mass spectrometry is an automated, fast, and highly accurate alternative to capillary sequencing.