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At least 1,243 records · Page 69Linked to original sources
PubMed1991

Application of aqueous two-phase partition in PEG-phosphate systems. Design and implementation of a prototype process for recovery of bulk protein fractions from waste brewer's yeast.

The practical development of a process exploiting aqueous two-phase partition in PEG/phosphate systems is described for the recovery and partial purification of a bulk protein fraction from waste Brewer's yeast. Inadequacies in current assumptions concerning de novo process design of such systems necessitated the empirical establishment of conditions for the two-step extraction of protein from wet-milled yeast suspensions. Experiments with homogeneous proteins and yeast extracts are presented to illustrate the true influence of phase volume upon primary protein extraction, and of added salts and modified system pH upon selective back extraction. A mechanistic description of physical and chemical factors influential upon selective phase partition in PEG/phosphate systems is discussed.

Fungal Proteins↗
PubMed2026

Benchmarking DNA extraction protocols across use cases for culture-independent Nanopore metagenomics.

Oxford Nanopore Technologies (ONT) sequencing offers several advantages for metagenomics, including long reads, rapid turnaround, low upfront cost, scalability and portability. However, for ONT metagenomics, DNA yield, quality and integrity are important considerations when selecting an extraction method. Many metagenomic extraction methods use harsh lysis conditions to extract a wide range of species and provide an accurate community composition, but these conditions can compromise DNA fragment length. Therefore, extraction methods for ONT metagenomics must balance DNA shearing and recovery with representative community lysis. We systematically evaluated DNA extraction methods for ONT metagenomic sequencing using a use case-oriented framework. Among nearly 50 extraction methods screened, 7 were selected for detailed comparison based on suitability for metagenomics, variation in methodology, availability, cost and processing time: Norgen BioTek Corp's Stool DNA Isolation (NG), Zymo Research's ZymoBIOMICS Quick-DNA HMW MagBead (ZMG), Qiagen's DNeasy Blood and Tissue (QBT), Macherey-Nagel's NucleoMag DNA Microbiome (MN), Zymo Research's ZymoBIOMICS DNA Mini Prep (ZMI), Qiagen's DNeasy PowerSoil/QIAamp PowerFecal Pro (PS) and Qiagen's QIAamp Fast DNA Stool Mini (QIA). Methods were tested using Zymo Research's ZymoBIOMICS Microbial Community Standard (MCS), a matrix-free mock community with known composition. DNA extracts were sequenced on an ONT PromethION using the Rapid Barcoding Kit, except QIA due to insufficient DNA yield. Metrics for the method, DNA extracts, sequencing and genomes were evaluated, revealing trade-offs between methods. The two magnetic bead methods, MN and ZMG, produced the highest mean read length N50 values (13.9 and 16.5 kb, respectively) but showed apparent community compositions skewed towards Gram-negative bacteria. In contrast, ZMI and PS maintained a community composition close to expected, with reduced mean read length N50 values (4.5 vs. 7.5 kb). Performance across various metrics is presented in the context of the following use cases: maximizing genome coverage and assembly completeness, preserving composition accuracy, targeting specific species and limiting required resources (equipment, time or budget). The metrics and use case considerations presented offer practical guidance for informed selection of DNA extraction methods for ONT metagenomics. For accurate community composition, ZMI or PS are recommended, while PS and ZMG perform best at maximizing genome coverage and assembly completeness. NG and QBT may be the most economical options, though performance trade-offs were observed. Finally, PS may be the preferred method for time-sensitive diagnostic or field applications.

Metagenomics↗
PubMed2006

The screening analysis of antiradical activity of some plant extracts.

INTRODUCTION: There is a need for screening studies in order to select plant extracts or plant raw materials with strong antiradical activity which could be used as medicines or substances to protect food from oxidation. In this paper the antiradical activities of some plant raw materials were investigated. MATERIAL/METHODS: The intensity of antiradical activity of extracts was investigated using DPPH* (1,1-diphenyl-2-picrylhydrazyl) radical as a substrate. The antiradical activity unit was defined and the number of antiradical activity units EAU(515) per 1 mg of plant extract and TAU(515) per 1 g of plant raw materials were calculated. Plant extracts were obtained with a methanol or methanol-water (1:1) solution. RESULTS AND DISCUSSION: The highest numbers of antiradical activity units EAU(515) were found for ethyl acetate extracts from the leaves of green and black tea. The lowest EAU(515) value was demonstrated for garlic extracts. When the number of activity units TAU(515) was calculated per 1 g of raw material, the highest value was found for the leaves of green tea, much lower for bee propolis and the leaves of black tea. On the basis of the presented results, green tea leaves, bee propolis, and the leaves of black tea could be considered as potential sources of extracts with strong antiradical activity.

Antioxidants↗
PubMed2005

Extracting data recorded with OpenSDE: possibilities and limitations.

PURPOSE: OpenSDE is an application intended to support structured data entry in a variety of settings, such as routine care and clinical research. The past years development has focused on data entry to support expressiveness and flexibility. The focus is now shifting to data extraction: what are the possibilities for extracting the data and does the adopted strategy pose limitations? METHODS: Data extraction is supported by presenting the concepts for extraction in the same tree structure as for data entry. Users can select all or a sub selection of these concepts for extraction. Selected concepts are extracted and converted to a table format that can be queried using conventional tools. RESULTS: The extraction tool (entity export) provides a successful technical solution for data extraction. Using the extracted data, however, leads to obstacles that are a result of a fundamental design principle of OpenSDE.

Computer Simulation↗
PubMed2006

[Analysis of pesticide multiresidues in rice by gas chromatography-mass spectrometry coupled with solid phase extraction].

A new analytical method was developed to simultaneously determine multiple pesticide residues in rice including organophosphorus, organochlorine, carbamate and pyrethroid. First, the solvents for pesticide extraction were selected for optimization. Eight solvents were screened to find that the extraction efficiency with dichloromethane was the best. Second, clean-up was performed by solid phase extraction using a Florisil cartridge. Various mixtures of hexane and acetone were tested to show that the mixture of hexane-acetone (4:1, v/v) had the best performance. The clean-up helped the sample purification significantly. The prepared sample was analyzed using gas chromatography-mass spectrometry (GC-MS) in selected ion monitoring (SIM) mode. The pesticides were identified with retention time and selected ions and their relative abundances, and they were quantified based on extract of spiking standards in a blank sample. The limits of detection (LODs) were evaluated on the values of the lower concentration fortified sample under the signal-to-noise ratio of 3:1. The recoveries and relative standard deviations (RSDs) were checked by adding pesticide standard solution at two levels to untreated samples, and the triplicate analysis of the samples were carried out for each spiked level. The LODs were at microg/kg level. The average recoveries of most pesticides were from 75% to 120 %. The RSDs were less than 10.4% (n = 3). These results indicated that this method is simple, rapid, sensitive for the simultaneous determination requirements of multiple pesticide residues in rice.

Food Contamination↗
PubMed2003

A high-yield method to extract peptides from rat brain tissue.

A process to extract and enrich extracellular peptides and proteins from tissues should have broad utility in the burgeoning proteomics field. To address this need, a novel three-step protocol was developed to extract polypeptides from whole tissue samples and enrich the extracellular components. The initial homogenization of rat brain was carried out at neutral pH to optimize protein and peptide stability and solubility. Subsequent covalent chromatography on an activated thiopropyl resin was employed to debulk the tissue extract by selectively removing a substantial fraction of the intracellular protein component under nondenaturing conditions. Finally, extraction with 0.1% trifluoroacetic acid was used to selectively precipitate large proteins while enhancing the solubility of smaller proteins and peptides. The fractions from each step in the process were compared to a single extract obtained by homogenization in 0.5 M acetic acid. The recovery and yields of endogenous neuropeptides and an exogenously added peptide were evaluated by enzyme immunoassay and Western blotting, respectively. In summary, the three-step protocol was superior to the extraction of tissue with 0.5 M acetic acid in terms of peptide recovery, enrichment, and sample stability. Enrichment of the extracellular protein compartment from tissues should be valuable in proteomics experiments aimed at identifying biomarkers that can partition into serum.

Animals↗
PubMed2006

Vanadium recovery from oil fly ash by leaching, precipitation and solvent extraction processes.

In order to reduce the environmental impact due to land disposal of oil fly ash from power plants and to valorize this waste material, the removal of vanadium was investigated using leaching processes (acidic and alkaline treatments), followed by a second step of metal recovery from leachates involving either solvent extraction or selective precipitation. Despite a lower leaching efficiency (compared to sulfuric acid), sodium hydroxide was selected for vanadium leaching since it is more selective for vanadium (versus other transition metals). Precipitation was preferred to solvent extraction for the second step in the treatment since: (a) it is more selective; enabling complete recovery of vanadate from the leachate in the form of pure ammonium vanadate; and (b) stripping of the loaded organic phase (in the solvent extraction process) was not efficient. Precipitation was performed in a two-step procedure: (a) aluminum was first precipitated at pH 8; (b) then ammonium chloride was added at pH 5 to bring about vanadium precipitation.

Aluminum↗
PubMed1996

Determination of alkylphenols and linear alkylbenzene sulfonates in sediments applying accelerated solvent extraction (ASE).

A time and solvent saving method (accelerated solvent extraction, ASE) for the extraction of anionic surfactants as linear alkylbenzene sulfonates (LAS) and alkylphenols from sediments is presented. The analytes are extracted by methanol at 100 degrees C and 150 atm within 10 min of static and 5 min of dynamic extraction. The presence of methanol and a maximum pressure of 150 atm are essential for the complete extraction of anionic surfactants, whereas the extraction of alkylphenols is independent of both parameters. The extraction of alkylphenolethoxylates yielded only unsatisfactor results. It was demonstrated that the ASE extraction is selective for LAS surfactants, while matrix substances, which are extracted by the methanol extraction and interfere with the target analytes during the HPLC-run, remain in the sample. Thus, a further clean-up procedure of the ASE extract is not necessary.

Journal Article↗
PubMed1998

Amebicidal activity of plant extracts from Southeast Asia on Acanthamoeba spp.

The effect of 100 polar and 100 nonpolar plant extract materials obtained from Southeast Asia were evaluated for amebicidal activity in vitro against three species of Acanthamoeba. A. culbertsoni, A. castellanii, and A. polyphaga, the causative agents of granulomatous amebic encephalitis and amebic keratitis, were studied in vitro to determine whether the plant extracts exhibited amebicidal activity or induced encystment of the amebae. Of the 200 plant extracts tested, extracts obtained from three plants (Ipomoea sp., Kaempferia galanga, and Cananga odorata) were amebicidal for all three species of Acanthamoeba and a fourth extract prepared from Gastrochilus panduratum was lytic for A. polyphaga and growth-inhibitory for A. castellanii and A. culbertsoni. Three plant extracts induced encystment of all three species of Acanthamoeba. Select plant extracts were tested as well for tumoricidal activity against B103 neuroblastoma cells. Some plant extracts that exhibited tumoricidal activity for B103 cells were not amebicidal for Acanthamoeba spp. Additionally, the polar and nonpolar extracts that exhibited amebicidal activity were also tested for activity against primary murine peritoneal macrophage cultures. Plant extracts that demonstrated tumoricidal or amebicidal activity were not lytic for normal macrophage cultures.

Acanthamoeba↗
PubMed1991

Detection and characterization of a factor which rescues spliceosome assembly from a heat-inactivated HeLa cell nuclear extract.

Mild heat treatment of HeLa cell nuclear extracts (NE) selectively inhibits pre-mRNA splicing. Heat-inactivated extracts can be complemented by a small amount of untreated NE. Utilizing this complementation assay and a combination of ion-exchange, affinity, and hydrophobic chromatography, a heat reversal factor (HRF) was purified from NE that is required to rescue pre-mRNA splicing from a heat-inactivated extract. This activity in its most purified form consistently copurified in a fraction containing two 70-kDa proteins and a minor polypeptide of approximately 100 kDa. It was free of the major small nuclear RNAs, sensitive to protease, and required to rescue spliceosome formation from a heat-inactivated nuclear extract. These results suggest that this factor is a protein that may be an important component in pre-mRNA splicing, or alternatively, it may be involved in renaturation of a heat-sensitive splicing factor.

Cell Nucleus↗
PubMed1984

Evidence for two RNA polymerase activities in Euglena gracilis chloroplasts.

Two types of RNA polymerase activity were isolated from Euglena gracilis chloroplasts and compared. One polymerase is tightly bound to chloroplast DNA; this complex is called the transcriptionally active chromosome (TAC) (Rushlow, K. E., Orozco, E. M., Jr., Lipper, C., and Hallick, R. B. (1980) J. Biol. Chem. 255, 3786-3792). The other activity is found in a soluble extract of Euglena chloroplasts. The soluble extract is dependent upon an exogenous DNA template for activity. The two activities can be isolated in two distinct subchloroplast fractions from a single chloroplast preparation. The soluble extract is selective for transcription of transfer RNA genes, whereas the TAC is selective for ribosomal RNA genes. TAC and the soluble extract respond differently to KCl and Mg2+. The soluble extract is sensitive to heparin, and TAC is resistant. The two activities have different temperature optima. Based on this evidence, we conclude that Euglena chloroplasts have at least two distinct RNA polymerase activities.

Base Sequence↗
PubMedDate not supplied

Discovery and development of anticancer agents from plants.

A novel in vitro assay for the discovery of anticancer agents was used to examine aqueous and organic extracts from 1847 plants collected mainly in the U.S. Southwest and West. The assay results were separated into 5 categories: inactive (62%), equally active (36%), equally active and potent (0.5%), solid tumor selective (1.4%), and human selective (0.8%). Extracts from the latter three categories were fractionated using the in vitro assay to biodirect each step. Psorothamnus emoryi extracts were solid tumor selective and yielded two active compounds upon fractionation: dalrubone and 5-methoxydalrubone. Calocedrus decurrens was equally active and potent and yielded deoxypodophyllotoxin as the active compound. Linanthus floribundus was human selective and yielded strophanthidin as the active compound. The potential of this assay to discover novel anticancer agents from the active extracts is discussed.

Animals↗
PubMed1993

Alternative 3' splice-site selection using HeLa cell nuclear extracts prepared with high-ionic buffers.

To investigate the role of cellular trans-acting factors in alternative 3' splice-site selection, a series of HeLa cell nuclear extracts were generated with salt washes ranging from 0.4 to 0.8 M salt. These extracts were tested with human beta-globin pre-mRNAs containing tandem 5' or 3' splice-site duplications as the substrates. High-salt (0.6 M and higher)-based buffers generated nuclear extracts that differentially processed pre-mRNAs containing competing 3' splice sites. High-salt extracts increased the usage of the distal 3' splice site, whereas no shift in 5' splice-site usage could be detected. Western analysis suggested that this shift in alternative 3' splice-site selection was not due to changes in the U2 snRNP auxiliary factor or polypyrimidine tract-binding protein levels.

Alternative Splicing↗
PubMed1998

[Development of antiviral therapeutic agents from traditional medicines].

Traditional medicines contain various metabolites derived from nucleic acid, protein, and lipid metabolism. Some of these specific metabolites may recognize the differences between viral and host metabolism resulting in anti-viral activity; hence traditional medicines may be useful sources for new antiviral agents. Traditional medicines can be cheaply obtained and have been orally administered as hot-water extracts. Therefore, they may be used for the prophylactic and therapeutic treatment of viral infection by drinking them, such as coffee or tea. Here we describe how the antiviral activity of traditional medicines was screened in vitro and how their therapeutic antiviral activities were verified in vivo, to obtain traditional antiviral medicines that can be clinically used. Therefore, we have selected 12 herbal extracts, from more than 250 herbal medicines, that exhibit therapeutic activities against cutaneous herpes simplex virus (HSV) type 1 (HSV-1) infection in mice. Four of the 12 augmented the therapeutic efficacy of acyclovir (ACV) in mice and showed potent anti-HSV activity against infection with ACV-resistant HSV-1 mutants in mice. These herbal extracts selectively inhibited viral DNA synthesis and showed a different mode of anti-HSV-1 action from that of ACV. They were also effective against both recurrent HSV and cytomegalovirus infections, without toxicity. Such prophylactic and therapeutic antiviral activities of the traditional medicines were verified by the purification of major active compounds. We could show new indications of traditional medicines as antiviral agents. Thus, the drinking of the extracts, in a daily tea or coffee, may be used for prophylaxis and therapy of diseases caused by herpes virus infection and improve the quality of life.

Animals↗
PubMed2005

Validated application of a new high-performance liquid chromatographic method for the determination of selected flavonoids and phenolic acids in human plasma using electrochemical detection.

We developed a sensitive method for determination of 23 flavonoids and phenolic acids, which represent phenolic acids and five subclasses of flavonoids. Plasma samples were extracted with selective solid-phase-extraction columns and separated by RP-high-performance liquid chromatography (HPLC). For detection an electrochemical detector was used. Identification and test of purity were carried out via retention times and spectra analyses. Limits of detection varied from 1.45 to 22.27 nmol/l. Recovery varied from 81% to 106%. Reproducibility for all analytes was below 10% (coefficient of variation, CV (%)) and ranged between 3.1% and 9.8%. This method can be applied to samples from interventional studies as well as observational studies.

Chromatography, High Pressure Liquid↗
PubMedDate not supplied

Determination of palladium in gasoline by neutron activation analysis and automated column extraction.

Palladium in gasoline was determined by means of neutron activation analysis (NAA) and selective sorbent extraction. Unleaded gasoline consistent with DIN EN 228, RON 95 was irradiated at a thermal neutron flux of phith = 1.68 x 10(13)s(-1)cm(-2) and an epithermal neutron flux of 3.32 x 10(11)s(-1)cm(-2) for t(irr) = 12 h. The irradiated gasoline was digested with nitric acid and palladium was then separated as N,N-diethyl-N'-benzoylthiourea complex by an automated column pre-concentration procedure. The eluate of 50 microL was dried on a filter paper and the 88.03 keV photons resulting from the decay of 109Pd were detected in a low level HPGe spectrometer with an efficiency of 35.5%. Severe interferences with other matrix constituents, especially 82Br could be overcome and the detection limit for palladium was improved to 3.4 ng/L at a confidence level of 90%. Although the analytical procedure applied yielded the lowest detection limit for palladium obtained in gasoline up to now, no indications for the presence of palladium were found.

Journal Article↗