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The extraction of cell walls of Pseudomonas aeruginosa with aqueous phenol. The insoluble residue and material from the aqueous layers.

ABSTRACT: 1. The insoluble residue and material present in the aqueous layers resulting from treatment of cell walls of Pseudomonas aeruginosa with aqueous phenol were examined. 2. The products (fractions AqI and AqII) isolated from the aqueous layers from the first and second extractions respectively account for approx. 25% and 12% of the cell wall and consist of both lipopolysaccharide and muropeptide. 3. The lipid part of the lipopolysaccharide is qualitatively similar to the corresponding material (lipid A) from other Gram-negative organisms, as is the polysaccharide part. 4. The insoluble residue (fraction R) contains sacculi, which also occur in fraction AqII. On hydrolysis, the sacculi yield glucosamine, muramic acid, alanine, glutamic acid and 2,6-diaminopimelic acid, together with small amounts of lysine, and they are therefore similar to the murein sacculi of other Gram-negative organisms. Fraction R also contains substantial amounts of protein, which differs from that obtained from the phenol layer. 5. The possible association or aggregation of lipopolysaccharide, murein and murein sacculi is discussed.

SUBMITTER: Clarke K

PROVIDER: S-EPMC1198376 | biostudies-other | 1967 Nov

REPOSITORIES: biostudies-other

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The extraction of cell walls of Pseudomonas aeruginosa with aqueous phenol. Material from the phenol layer.

Project description:1. A method is described for the fractionation of cell walls of Pseudomonas aeruginosa by using aqueous phenol. 2. With this technique, cell walls are quantitatively separated into five fractions: two water-soluble fractions (AqI and AqII), a residual insoluble fraction (R), and two phenol-soluble fractions (PhMP and PhMS). 3. The compositions of fractions PhMP and PhMS are discussed. Fraction PhMP consists almost entirely of protein, which is soluble in aqueous sodium dodecyl sulphate. Analytical ultracentrifugation of the solution yields a single peak, but several components may be resolved by gel electrophoresis. 4. Fraction PhMS consists principally of phospholipid (approx. 44%) and fatty acids (approx. 27%), although smaller amounts (approx. 13%) of protein are present.

| S-EPMC1198375 | biostudies-other

The cell walls of Pseudomonas aeruginosa. General composition.

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| S-EPMC1198374 | biostudies-other

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Polypropylene as a Retrofitting Material for Shear Walls.

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Optimization of phenol-chloroform RNA extraction.

Project description:Accurate and reliable analysis of gene expression depends on the extraction of pure and high-quality RNA. However, while the conventional phenol-chloroform RNA extraction is preferable over silica-based columns, particularly when cost is a concern or higher RNA yield is desired, it can result in significant RNA contamination. Contaminants including excess phenol, chloroform, or salts, can have significant impacts on downstream applications, including RNA quantification and reverse transcription, that can skew data collection and interpretation. To overcome the issue of RNA contamination in the conventional phenol-chloroform based RNA extraction method, we have optimized the protocol by adding one chloroform extraction step, and several RNA washing steps. Importantly, RNA quality and purity and accuracy in the quantification of RNA concentration were significantly improved with the modified protocol, resulting in reliable data collection and interpretation in downstream gene expression analysis. •Our protocol is customized by the addition of a second chloroform extraction step. Chloroform is carefully pipetted so as to not disturb the interphase layer. Any contaminants accidentally removed from interphase will be present in subsequent steps and can result in RNA contaminated with protein or phenol. The additional chloroform step increases RNA purity.•Additionally, the addition of 2 additional ethanol washes, initially intended to remove any residual salts from the isopropanol RNA precipitation step, also removed residual phenol contamination, enhancing RNA purity.•In summary, these modifications serve to enhance not only the purity of the RNA but, also increase the accuracy and reliability of RNA quantification.

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PTex - Purification of Cross-linked RNA-Protein Complexes by Phenol-Toluol Extraction

Project description:PTex is a protocol to purify UV-cross-linked ribonucleoproteins (RNPs) in an unbiased and sequence-independent fashion. Total RNA from HEK293 cells was analysed by RNASeq from whole cell lysates as well as after purification of RNPs.

2019-02-02 | GSE113655 | GEO

Mutation of a distal gating residue modulates NADH binding in NADH:Quinone oxidoreductase from Pseudomonas aeruginosa PAO1.

Project description:Enzymes require flexible regions to adopt multiple conformations during catalysis. The mobile regions of enzymes include gates that modulate the passage of molecules in and out of the enzyme's active site. The enzyme PA1024 from Pseudomonas aeruginosa PA01 is a recently discovered flavin-dependent NADH:quinone oxidoreductase (NQO, EC 1.6.5.9). Q80 in loop 3 (residues 75-86) of NQO is ∼15 Å away from the flavin and creates a gate that seals the active site through a hydrogen bond with Y261 upon NADH binding. In this study, we mutated Q80 to glycine, leucine, or glutamate to investigate the mechanistic significance of distal residue Q80 in NADH binding in the active site of NQO. The UV-visible absorption spectrum reveals that the mutation of Q80 minimally affects the protein microenvironment surrounding the flavin. The anaerobic reductive half-reaction of the NQO-mutants yields a ≥25-fold increase in the Kd value for NADH compared to the WT enzyme. However, we determined that the kred value was similar in the Q80G, Q80L, and wildtype enzymes and only ∼25% smaller in the Q80E enzyme. Steady-state kinetics with NQO-mutants and NQO-WT at varying concentrations of NADH and 1,4-benzoquinone establish a ≤5-fold decrease in the kcat/KNADH value. Moreover, there is no significant difference in the kcat/KBQ (∼1 × 106 M-1s-1) and kcat (∼24 s-1) values in NQO-mutants and NQO-WT. These results are consistent with the distal residue Q80 being mechanistically essential for NADH binding to NQO with minimal effect on the quinone binding to the enzyme and hydride transfer from NADH to flavin.

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Project description:The relatively thick primary walls of epidermal and collenchyma cells often form waviness on the surface that faces the protoplast when they are released from the tensile in-plane stress that operates in situ. This waviness is a manifestation of buckling that results from the heterogeneity of the elastic strain across the wall. In this study, this heterogeneity was confirmed by the spontaneous bending of isolated wall fragments that were initially flat. We combined the empirical data on the formation of waviness in growing cell walls with computations of the buckled wall shapes. We chose cylindrical-shaped organs with a high degree of longitudinal tissue stress because in such organs the surface deformation that accompanies the removal of the stress is strongly anisotropic and leads to the formation of waviness in which wrinkles on the inner wall surface are always transverse to the organ axis. The computations showed that the strain heterogeneity results from individual or overlaid gradients of pre-stress and stiffness across the wall. The computed wall shapes depend on the assumed wall thickness and mechanical gradients. Thus, a quantitative analysis of the wall waviness that forms after stress removal can be used to assess the mechanical heterogeneity of the cell wall.

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Heat- and Ultrasound-Assisted Aqueous Extraction of Soluble Carbohydrates and Phenolics from Carob Kibbles of Variable Size and Source Material.

Project description:Aqueous extraction of carob kibbles is the fundamental step in the production of carob juice and carob molasses. Improving the theoretical yield in sugars during organic solvent-free aqueous extraction is of prime interest to the food industry. Collateral extraction of phenolics, however, must be monitored as it influences the sensory and functional profile of carob juice. We presently examined the impact of source material, kibble size, temperature, and duration on the efficiency of extracting sugars and phenolics aqueously by conventional heat-assisted (HAE) and ultrasound-assisted (UAE) methods. Source material was the most influential factor determining the concentration of phenolics extracted by either method. Source material also influenced the relative proportions of sucrose, glucose, and fructose, which may impact the perceived sweetness of the juice. Kibble size (medium size M = 9-13 mm; powder size P = 1-4 mm) was more influential with UAE than HAE for both sugars and phenolics but was rendered less influential with prolonged UAE duration. Increasing HAE temperature (from 25 °C to 75 °C) favored the extraction of phenolics over sugars; however, prolonging extraction at 25 °C improved sugar yield without excessive yield in phenolics. Disproportionate extraction of phenolics over sugars limits the use of heat-assisted extraction to improve sugar yield in carob juice production and may shift the product's sensory profile toward astringency. Prolonged extraction at near ambient temperature can, however, improve sugar yield, keeping collateral extraction of phenolics low. Ultrasound agitation constitutes an effective means of extracting sugars from powder-size kibbles. Industrial application of both methodologies depends on the targeted functional and sensory properties of carob juice.

| S-EPMC7599798 | biostudies-literature

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