Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ACCESS DATA

Json Xml

Similar Datasets

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.

Project description:1. Cell walls of Pseudomonas aeruginosa were prepared and analysed. 2. Separate preparations were found to be reproducible, e.g. the phosphorus contents of all batches lay in the range 2.0-2.1%. 3. Ninhydrin-positive compounds in hydrolysates accounted for 43-46% of the cell wall and 79-87% of the nitrogen of the cell wall. Examination of the results for individual ninhydrin-positive compounds showed that 5-15% of the cell wall was murein and about 30% protein. 4. Trypsin treatment of crude cell-wall preparations preferentially liberated arginine, lysine and leucine, but it was not clear whether these arose from cell-wall or cytoplasmic proteins.

| S-EPMC1198374 | biostudies-other

A green hydrophobic deep eutectic solvent for extraction of phenol from aqueous phase.

Project description:Deep eutectic solvents (DESs), have been recognized as effective materials for the extraction of different compounds. In this study, the performance of a novel hydrophobic DES was evaluated for the extraction of phenol from aqueous solutions. Octanoic and dodecanoic fatty acid precursors with a definite molar ratio of 3:1, respectively, were used for the DES having a low melting point of 8.3 °C. The purity and stability of the product were confirmed via characterizing by FTIR, 1H and 13C NMR methods. The liquid-liquid equilibrium of the water + phenol + DES ternary system at different temperatures of 293.2, 298.2 and 308.2 K was accordingly studied through cloud point titration method and refractive index measurement. Interestingly, the important parameters of the solute distribution coefficient and the separation factor were, respectively, within the high levels of (6.8321-9.7787) and (895.76-2770.17), indicating the amazing capability of the DES. Reasonably, both of these parameters decreased with temperature. The NRTL and UNIQUAC thermodynamic models were employed to reproduce the obtained tie-lines and to determine the interaction parameters at each temperature. The low level root mean square deviations for the mentioned models were, respectively, within (0.0014-0.0027) and (0.0045-0.0063); confirming satisfactorily agreement with the experimental data.

| S-EPMC10576737 | biostudies-literature

Nonidet P-40 extraction of lymphocyte plasma membrane. Characterization of the insoluble residue.

Project description:Purified preparations of lymphocyte plasma membrane were extracted exhaustively with Nonidet P-40 in Dulbecco's phosphate-buffered saline medium. The insoluble fraction, as defined by sedimentation at 10(6) g-min, contained about 10% of the membrane protein as well as cholesterol and phospholipid. The lipid/protein ratio, cholesterol/phospholipid ratio and sphingomyelin content were increased in the residue. Density-gradient centrifugation suggested that the lipid and protein form a common entity. As judged by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis, the Nonidet P-40-insoluble fractions of the plasma membranes of human B lymphoblastoid cells and pig mesenteric lymph-node lymphocytes possessed similar qualitative polypeptide compositions but differed quantitatively. Both residues comprised major polypeptides of Mr 28 000, 33 000, 45 000 and 68 000, together with a prominent band of Mr 120 000 in the human and of Mr 200 000 in the pig. The polypeptides of Mr 28 000, 33 000, 68 000 and 120 000 were probably located exclusively in the Nonidet P-40-insoluble residue, which also possessed a 4-fold increase in 5'-nucleotidase specific activity. The results indicate that a reproducible fraction of lymphocyte plasma membrane is insoluble in non-ionic detergents and that this fraction possesses a unique polypeptide composition. By analogy with similar studies with erythrocyte ghosts, it appears likely that the polypeptides are located on the plasma membrane's cytoplasmic face.

| S-EPMC1153477 | biostudies-other

Polypropylene as a Retrofitting Material for Shear Walls.

Project description:In recent years, on account of their excellent mechanical properties, composite materials (made of epoxy-bonded carbon, glass, or aramid fibers) have been used to reinforce masonry walls against in-plane actions. These materials have proven to be an effective solution for the strengthening of unreinforced masonry (URM) walls. Lately, research has shifted to the study of different types of fibers to avoid the use of epoxy adhesives, whose long-term behavior and compatibility with masonry are poor. This paper describes an experimental program that investigated the behavior of URM shear walls strengthened with two types of commercially available polypropylene products: short fibers (fiber length = 12 mm) and polypropylene nets. This investigation aimed to evaluate the influence of polypropylene reinforcement, embedded into an inorganic matrix, in terms of the improvement of the lateral load-carrying capacity, failure mechanism, ductility, and energy dissipation capacity of URM wall panels, where nine walls were subjected to in-plane loads using a racking test setup. The study showed that using two layers of polypropylene fibers embedded into a cementitious matrix greatly increased the in-plane load capacity of the brickwork masonry. On the other hand, the test results indicated that polypropylene nets, used as a repair method for cracked shear walls, cannot improve the structural performance of the walls.

| S-EPMC7321489 | biostudies-literature

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.

| S-EPMC6031757 | biostudies-literature

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.

| S-EPMC10033279 | biostudies-literature

Growing cell walls show a gradient of elastic strain across their layers.

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.

| S-EPMC6093493 | biostudies-literature

Evaluation of DNA Extraction Methods for Reliable Quantification of Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa

Project description:Detection and quantification of DNA biomarkers relies heavily on the yield and quality of DNA obtained by extraction from different matrices. Although a large number of studies have compared the yields of different extraction methods, the repeatability and intermediate precision of these methods have been largely overlooked. In the present study, five extraction methods were evaluated, using digital PCR, to determine their efficiency in extracting DNA from three different Gram-negative bacteria in sputum samples. The performance of two automated methods (GXT NA and QuickPick genomic DNA extraction kit, using Arrow and KingFisher Duo automated systems, respectively), two manual kit-based methods (QIAamp DNA mini kit; DNeasy UltraClean microbial kit), and one manual non-kit method (CTAB), was assessed. While GXT NA extraction kit and the CTAB method have the highest DNA yield, they did not meet the strict criteria for repeatability, intermediate precision, and measurement uncertainty for all three studied bacteria. However, due to limited clinical samples, a compromise is necessary, and the GXT NA extraction kit was found to be the method of choice. The study also showed that dPCR allowed for accurate determination of extraction method repeatability, which can help standardize molecular diagnostic approaches. Additionally, the determination of absolute copy numbers facilitated the calculation of measurement uncertainty, which was found to be influenced by the DNA extraction method used.

| S-EPMC10136035 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data