Browse
Submit Data
Databases
API
Help

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Screening Method for Polyhydroxyalkanoate Synthase Mutants Based on Polyester Degree of Polymerization Using High-Performance Liquid Chromatography.

ABSTRACT: A high-throughput screening method based on the degree of polymerization (DP) of polyhydroxyalkanoate (PHA) was developed using high-performance liquid chromatography (HPLC). In this method, PHA production was achieved using recombinant Escherichia coli supplemented with benzyl alcohol as a chain terminal compound. The cultured cells containing benzyl alcohol-capped PHA were decomposed by alkaline treatment, and the peaks of the decomposed monomer and benzyl alcohol were detected using HPLC. The DP of PHA could be determined from the peak ratio of the decomposed monomer to terminal benzyl alcohol. The measured DP was validated by other instrumental analyses using purified PHA samples. Using this system, mutants of PHA synthase from Bacillus cereus YB-4 (PhaRC_YB4) were screened, and some enzymes capable of producing PHA with higher DP than the wild-type enzyme were obtained. The PHA yields of two of these enzymes were equivalent to the yield of the wild-type enzyme. Therefore, this screening method is suitable for the selection of beneficial mutants that can produce high molecular weight PHAs.

SUBMITTER: Ishii-Hyakutake M

PROVIDER: S-EPMC8469876 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

A Liquid Chromatography/Mass Spectrometry Method for Screening Disulfide Tethering Fragments.

Project description:We report the refinement of a high-throughput, liquid chromatography/mass spectrometry (LC/MS)-based screening method for the identification of covalent small-molecule binders to proteins. Using a custom library of 1600 disulfide-capped fragments targeting surface cysteine residues, we optimize sample preparation, chromatography, and ionization conditions to maximize the reliability and flexibility of the approach. Data collection at a rate of 84 s per sample balances speed with reliability for sustained screening over multiple, diverse projects run over a 24-month period. The method is applicable to protein targets of various classes and a range of molecular masses. Data are processed in a custom pipeline that calculates a percent bound value for each compound and identifies false positives by calculating significance of detected masses (signal significance). An example pipeline is available through Biovia's ScienceCloud Protocol Exchange. Data collection and analysis methods for the screening of covalent adducts of intact proteins are now fast enough to screen the largest covalent compound libraries in 1 to 2 days.

| S-EPMC6609441 | biostudies-literature

Engineering of Aeromonas caviae Polyhydroxyalkanoate Synthase Through Site-Directed Mutagenesis for Enhanced Polymerization of the 3-Hydroxyhexanoate Unit

Project description:Polyhydroxyalkanoate (PHA) synthase is an enzyme that polymerizes the acyl group of hydroxyacyl-coenzyme A (CoA) substrates. Aeromonas caviae PHA synthase (PhaCAc) is an important biocatalyst for the synthesis of a useful PHA copolymer, poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] [P(3HB-co-3HHx)]. Previously, a PhaCAc mutant with double mutations in asparagine 149 (replaced by serine [N149S]) and aspartate 171 (replaced by glycine [D171G]) was generated to synthesize a 3HHx-rich P(3HB-co-3HHx) and was named PhaCAc NSDG. In this study, to further increase the 3HHx fraction in biosynthesized PHA, PhaCAc was engineered based on the three-dimensional structural information of PHA synthases. First, a homology model of PhaCAc was built to target the residues for site-directed mutagenesis. Three residues, namely tyrosine 318 (Y318), serine 389 (S389), and leucine 436 (L436), were predicted to be involved in substrate recognition by PhaCAc. These PhaCAc NSDG residues were replaced with other amino acids, and the resulting triple mutants were expressed in the engineered strain of Ralstonia eutropha for application in PHA biosynthesis from palm kernel oil. The S389T mutation allowed the synthesis of P(3HB-co-3HHx) with an increased 3HHx fraction without a significant reduction in PHA yield. Thus, a new workhorse enzyme was successfully engineered for the biosynthesis of a higher 3HHx-fraction polymer.

| S-EPMC7966705 | biostudies-literature

Development of a multi-class steroid hormone screening method using Liquid Chromatography/Tandem Mass Spectrometry (LC-MS/MS).

Project description:Monitoring complex endocrine pathways is often limited by indirect measurement or measurement of a single hormone class per analysis. There is a burgeoning need to develop specific direct-detection methods capable of providing simultaneous measurement of biologically relevant concentrations of multiple classes of hormones (estrogens, androgens, progestogens, and corticosteroids). The objectives of this study were to develop a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for multi-class steroid hormone detection using biologically relevant concentrations, then test limits of detection (LOD) in a high-background matrix by spiking charcoal-stripped fetal bovine serum (FBS) extract. Accuracy was tested with National Institute of Standards and Technology Standard Reference Materials (SRMs) with certified concentrations of cortisol, testosterone, and progesterone. 11-Deoxycorticosterone, 11-deoxycortisol, 17-hydroxypregnenolone, 17-hydroxyprogesterone, adrenosterone, androstenedione, cortisol, corticosterone, dehydroepiandrosterone, dihydrotestosterone, estradiol, estriol, estrone, equilin, pregnenolone, progesterone, and testosterone were also measured using isotopic dilution. Dansyl chloride (DC) derivatization was investigated maintaining the same method to improve and expedite estrogen analysis. Biologically relevant LODs were determined for 15 hormones. DC derivatization improved estrogen response two- to eight-fold, and improved chromatographic separation. All measurements had an accuracy ?14 % difference from certified values (not accounting for uncertainty) and relative standard deviation ?14 %. This method chromatographically separated and quantified biologically relevant concentrations of four hormone classes using highly specific fragmentation patterns and measured certified values of hormones that were previously split into three separate chromatographic methods.

| S-EPMC4906791 | biostudies-literature

Data preprocessing method for liquid chromatography-mass spectrometry based metabolomics.

Project description:A set of data preprocessing algorithms for peak detection and peak list alignment are reported for analysis of liquid chromatography-mass spectrometry (LC-MS)-based metabolomics data. For spectrum deconvolution, peak picking is achieved at the selected ion chromatogram (XIC) level. To estimate and remove the noise in XICs, each XIC is first segmented into several peak groups based on the continuity of scan number, and the noise level is estimated by all the XIC signals, except the regions potentially with presence of metabolite ion peaks. After removing noise, the peaks of molecular ions are detected using both the first and the second derivatives, followed by an efficient exponentially modified Gaussian-based peak deconvolution method for peak fitting. A two-stage alignment algorithm is also developed, where the retention times of all peaks are first transferred into the z-score domain and the peaks are aligned based on the measure of their mixture scores after retention time correction using a partial linear regression. Analysis of a set of spike-in LC-MS data from three groups of samples containing 16 metabolite standards mixed with metabolite extract from mouse livers demonstrates that the developed data preprocessing method performs better than two of the existing popular data analysis packages, MZmine2.6 and XCMS(2), for peak picking, peak list alignment, and quantification.

| S-EPMC3471364 | biostudies-literature

Toxic Cyanobacteria in Svalbard: Chemical Diversity of Microcystins Detected Using a Liquid Chromatography Mass Spectrometry Precursor Ion Screening Method.

Project description:Cyanobacteria synthesize a large variety of secondary metabolites including toxins. Microcystins (MCs) with hepato- and neurotoxic potential are well studied in bloom-forming planktonic species of temperate and tropical regions. Cyanobacterial biofilms thriving in the polar regions have recently emerged as a rich source for cyanobacterial secondary metabolites including previously undescribed congeners of microcystin. However, detection and detailed identification of these compounds is difficult due to unusual sample matrices and structural congeners produced. We here report a time-efficient liquid chromatography-mass spectrometry (LC-MS) precursor ion screening method that facilitates microcystin detection and identification. We applied this method to detect six different MC congeners in 8 out of 26 microbial mat samples of the Svalbard Archipelago in the Arctic. The congeners, of which [Asp³, ADMAdda⁵, Dhb⁷] MC-LR was most abundant, were similar to those reported in other polar habitats. Microcystins were also determined using an Adda-specific enzyme-linked immunosorbent assay (Adda-ELISA). Nostoc sp. was identified as a putative toxin producer using molecular methods that targeted 16S rRNA genes and genes involved in microcystin production. The mcy genes detected showed highest similarities to other Arctic or Antarctic sequences. The LC-MS precursor ion screening method could be useful for microcystin detection in unusual matrices such as benthic biofilms or lichen.

| S-EPMC5923313 | biostudies-literature

Reproducibility assessment for a broad spectrum drug screening method from urine using liquid chromatography time-of-flight mass spectrometry

Project description: Not available

| S-EPMC11322752 | biostudies-literature

Screening potential mitochondria-targeting compounds from traditional Chinese medicines using a mitochondria-based centrifugal ultrafiltration/liquid chromatography/mass spectrometry method.

Project description:Mitochondria regulate numerous crucial cell processes, including energy production, apoptotic cell death, oxidative stress, calcium homeostasis and lipid metabolism. Here, we applied an efficient mitochondria-based centrifugal ultrafiltration/liquid chromatography/mass spectrometry (LC/MS) method, also known as screening method for mitochondria-targeted bioactive constituents (SM-MBC). This method allowed searching natural mitochondria-targeting compounds from traditional Chinese medicines (TCMs), including Puerariae Radix (PR) and Chuanxiong Radix (CR). A total of 23 active compounds were successfully discovered from the two TCMs extracts. Among these 23 hit compounds, 17 were identified by LC/MS, 12 of which were novel mitochondria-targeting compounds. Among these, 6 active compounds were analyzed in vitro for pharmacological tests and found able to affect mitochondrial functions. We also investigated the effects of the hit compounds on HepG2 cell proliferation and on loss of cardiomyocyte viability induced by hypoxia/reoxygenation injury. The results obtained are useful for in-depth understanding of mechanisms underlying TCMs therapeutic effects at mitochondria level and for developing novel potential drugs using TCMs as lead compounds. Finally, we showed that SM-MBC was an efficient protocol for the rapid screening of mitochondria-targeting constituents from complex samples such as PR and CR extracts.

| S-EPMC6104153 | biostudies-literature

Solid-State Polymerization of Poly(Ethylene Furanoate) Biobased Polyester, II: An Efficient and Facile Method to Synthesize High Molecular Weight Polyester Appropriate for Food Packaging Applications.

Project description:The goal of this study was to synthesize, through a facile strategy, high molecular weight poly(ethylene furanoate) (PEF), which could be applicable in food packaging applications. The efficient method to generate PEF with high molecular weight consists of carrying out a first solid-state polycondensation under vacuum for 6 h reaction time at 205 °C for the resulting polymer from two-step melt polycondensation process, which is catalyzed by tetrabutyl titanate (TBT). A remelting step was thereafter applied for 15 min at 250 °C for the obtained polyester. Thus, the PEF sample was ground into powder, and was then crystallized for 6 h at 170 °C. This polyester is then submitted to a second solid-state polycondensation (SSP) carried out at different reaction times (1, 2, 3.5, and 5 h) and temperatures 190, 200, and 205 °C, under vacuum. Ultimately, a significant increase in intrinsic viscosity is observed with only 5 h reaction time at 205 °C during the second SSP being needed to obtain very high molecular weight PEF polymer greater than 1 dL/g, which sufficient for manufacturing purposes. Intrinsic viscosity (IV), carboxyl end-group content (⁻COOH), and thermal properties, via differential scanning calorimetry (DSC), were measured for all resultant polyesters. Thanks to the post-polymerization process, DSC results showed that the melting temperatures of the prepared PEF samples were steadily enhanced in an obvious way as a function of reaction time and temperature increase. It was revealed, as was expected for all SSP samples, that the intrinsic viscosity and the average molecular weight of PEF polyester increased with increasing SSP time and temperature, whereas the number of carboxyl end-group concentration was decreased. A simple kinetic model was also developed and used to predict the time evolution of polyesters IV, as well as the carboxyl and hydroxyl end-groups of PEF during the SSP.

| S-EPMC6415450 | biostudies-other

Fast screening of Depolymerized Lignin Samples Through 2D-Liquid Chromatography Mapping.

Project description:Lignin valorization and particularly its depolymerization into bio-aromatics, has emerged as an important research topic within green chemistry. However, screening of catalysts and reaction conditions within this field is strongly constrained by the lack of analytical techniques that allow for fast and detailed mapping of the product pools. This analytical gap results from the inherent product pool complexity and the focus of the state-of-the-art on monomers and dimers, overlooking the larger oligomers. In this work, this gap is bridged through the development of a quasi-orthogonal GPC-HPLC-UV/VIS method that is able to separate the bio-aromatics according to molecular weight (hydrodynamic volume) and polarity. The method is evaluated using model compounds and real lignin depolymerization samples. The resulting color plots provide a powerful graphical tool to rapidly assess differences in reaction selectivity towards monomers and dimers as well as to identify differences in the oligomers.

| S-EPMC8340071 | biostudies-literature

Development of the Microemulsion Electrokinetic Capillary Chromatography Method for the Analysis of Disperse Dyes Extracted from Polyester Fibers.

Project description:The study aimed to develop a method for the separation of dispersed dyes extracted from polyester fibers. Nine commercially available disperse dyes, which were used to dye three polyester fabrics, were tested. Extraction of dyes from 1 cm long threads was carried out in chlorobenzene at 100 °C for 6 h. The separation was performed using microemulsion electrokinetic capillary chromatography (MEEKC) with photodiode array detection. Microemulsion based on a borate buffer with an organic phase of n-octane and butanol and a mixture of surfactants, sodium dodecyl sulphate and sodium cholate, were used. The addition of isopropanol and cyclodextrins to microemulsion resulted in a notable improvement in resolution and selectivity. The content of additives was optimized by using the Doehlert experimental design. Values of the coefficient of variance obtained in the validation process, illustrating the repeatability and intermediate precision of the migration times fit in the range of 0.11-1.24% and 0.58-3.21%, respectively. The developed method was also successfully applied to the differentiation of 28 real samples-polyester threads collected from clothing. The obtained results confirmed that proposed method may be used in the discriminant analysis of polyesters dying by disperse dyes and is promisingly employable in forensic practice.

| S-EPMC9609498 | 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