Browse
Submit Data
Databases
API
Help

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Simple lysis of bacterial cells for DNA-based diagnostics using hydrophilic ionic liquids.

ABSTRACT: The extraction of nucleic acids from microorganisms for subsequent molecular diagnostic applications is still a tedious and time-consuming procedure. We developed a method for the rapid preparation of genomic DNA from bacteria based on hydrophilic ionic liquids (ILs). First, we tested eight ILs in different buffer systems for their inhibitory effects on quantitative PCR. The cell lysis potential of different IL/buffer combinations was assessed by application on Enterococcus faecalis as a model organism for Gram-positive bacteria. The two best ILs, choline hexanoate and 1-ethyl-3-methylimidazolium acetate, were compared with the reference enzymatic method and two commercial DNA extraction kits. All methods were evaluated on four Gram-positive and four Gram-negative bacterial species that are highly relevant for environmental, food, or clinical diagnostics. In comparison to the reference method, extraction yields of the IL-based procedure were within one order of magnitude for most of the strains. The final protocol for DNA extraction using the two ILs is very low-cost, avoids the use of hazardous chemicals and can be performed in five minutes on a simple heating block. This makes the method ideal for high sample throughput and offers the opportunity for DNA extraction from bacteria in resource-limited settings or even in the field.

SUBMITTER: Martzy R

PROVIDER: S-EPMC6768989 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Hydrophobic ionic liquids for quantitative bacterial cell lysis with subsequent DNA quantification.

Project description:DNA is one of the most frequently analyzed molecules in the life sciences. In this article we describe a simple and fast protocol for quantitative DNA isolation from bacteria based on hydrophobic ionic liquid supported cell lysis at elevated temperatures (120-150 °C) for subsequent PCR-based analysis. From a set of five hydrophobic ionic liquids, 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide was identified as the most suitable for quantitative cell lysis and DNA extraction because of limited quantitative PCR inhibition by the aqueous eluate as well as no detectable DNA uptake. The newly developed method was able to efficiently lyse Gram-negative bacterial cells, whereas Gram-positive cells were protected by their thick cell wall. The performance of the final protocol resulted in quantitative DNA extraction efficiencies for Gram-negative bacteria similar to those obtained with a commercial kit, whereas the number of handling steps, and especially the time required, was dramatically reduced. Graphical Abstract After careful evaluation of five hydrophobic ionic liquids, 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide ([BMPyr + ][Ntf 2- ]) was identified as the most suitable ionic liquid for quantitative cell lysis and DNA extraction. When used for Gram-negative bacteria, the protocol presented is simple and very fast and achieves DNA extraction efficiencies similar to those obtained with a commercial kit. ddH 2 O double-distilled water, qPCR quantitative PCR.

| S-EPMC5333376 | biostudies-literature

A new paradigm in sweat based wearable diagnostics biosensors using Room Temperature Ionic Liquids (RTILs).

Project description:Successful commercialization of wearable diagnostic sensors necessitates stability in detection of analytes over prolonged and continuous exposure to sweat. Challenges are primarily in ensuring target disease specific small analytes (i.e. metabolites, proteins, etc.) stability in complex sweat buffer with varying pH levels and composition over time. We present a facile approach to address these challenges using RTILs with antibody functionalized sensors on nanoporous, flexible polymer membranes. Temporal studies were performed using both infrared spectroscopic, dynamic light scattering, and impedimetric spectroscopy to demonstrate stability in detection of analytes, Interleukin-6 (IL-6) and Cortisol, from human sweat in RTILs. Temporal stability in sensor performance was performed as follows: (a) detection of target analytes after 0, 24, 48, 96, and 168 hours post-antibody sensor functionalization; and (b) continuous detection of target analytes post-antibody sensor functionalization. Limit of detection of IL-6 in human sweat was 0.2 pg/mL for 0-24 hours and 2 pg/mL for 24-48 hours post-antibody sensor functionalization. Continuous detection of IL-6 over 0.2-200 pg/mL in human sweat was demonstrated for a period of 10 hours post-antibody sensor functionalization. Furthermore, combinatorial detection of IL-6 and Cortisol in human sweat was established with minimal cross-talk for 0-48 hours post-antibody sensor functionalization.

| S-EPMC5434046 | biostudies-literature

Transcriptional toxicity of imidazolium- and cholinium-based ionic liquids

Project description:Ionic Liquids are a broad group of salts with low melting points that can be specifically tuned for a broad range of applications. Despite being initially considered “green” solvents, their better environmental friendliness compared to traditional solvents has been increasingly challenged. In this study, we aimed to investigate the molecular effects of ILs exposure by using RNA-sequencing to study differential gene expression patterns. Thus, we exposed Daphnia magna to 1-ethyl-3-methylimidazolium chloride ([C2mim]Cl), 1-dodecyl chloride-3-methylimidazolium ([C12mim]Cl) and cholinium chloride ([Chol]Cl). Results suggest that the three ILs share several mechanisms of toxicity, including cellular membrane and cytoskeleton damage, oxidative stress, inhibition of antioxidant enzymes, mitochondrial affectation, changes in protein biosynthesis and energy production, DNA damage, and ultimately, programmed cell death and disease initiation. Overall, the dataset revealed that [C2mim]Cl and [C12mim]Cl were, respectively, the least and the most toxic ILs at the transcriptional level. Also, it is reinforced that [Chol]Cl is not devoid of environmental hazardous potential. Unique gene expression signatures could also be identified for each IL.

2021-08-13 | GSE156769 | GEO

Simple observation of Streptococcus mutans biofilm by scanning electron microscopy using ionic liquids.

Project description:Scanning electron microscopy (SEM) has been successfully used to image biofilms because of its high resolution and magnification. However, conventional SEM requires dehydration and metal coating of biological samples before observation, and because biofilms consist mainly of water, sample dehydration may influence the biofilm structure. When coated with an ionic liquid, which is a kind of salt that exists in the liquid state at room temperature, biological samples for SEM observation do not require dehydration or metal coating because ionic liquids do not evaporate under vacuum conditions and are electrically conductive. This study investigates the ability of ionic liquids to allow SEM observation of Streptococcus mutans biofilms compared with conventional coating methods. Two hydrophilic and two hydrophobic ionic liquids, all of which are electronic conductors, are used. Compared with samples prepared by the conventional method, the ionic-liquid-treated samples do not exhibit a fibrous extracellular matrix structure and cracking on the biofilm surface. The hydrophilic ionic liquids give clearer images of the biofilm structure than those of the hydrophobic ionic liquids. This study finds that ionic liquids are useful for allowing the observation of biofilms by SEM without preparation by dehydration and metal coating.

| S-EPMC4305086 | biostudies-literature

Electrochemical Investigation of Curcumin-DNA Interaction by Using Hydroxyapatite Nanoparticles-Ionic Liquids Based Composite Electrodes.

Project description:Hydroxyapatite nanoparticles (HaP) and ionic liquid (IL) modified pencil graphite electrodes (PGEs) are newly developed in this assay. Electrochemical impedance spectroscopy (EIS), scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), and cyclic voltammetry (CV) were applied to examine the microscopic and electrochemical characterization of HaP and IL-modified biosensors. The interaction of curcumin with nucleic acids and polymerase chain reaction (PCR) samples was investigated by measuring the changes at the oxidation signals of both curcumin and guanine by differential pulse voltammetry (DPV) technique. The optimization of curcumin concentration, DNA concentration, and the interaction time was performed. The interaction of curcumin with PCR samples was also investigated by gel electrophoresis.

| S-EPMC8347690 | biostudies-literature

Flame Retardant-Functionalized Cotton Cellulose Using Phosphonate-Based Ionic Liquids.

Project description:Cellulose from cotton fibers was functionalized through a dissolution-regeneration process with phosphonate-based ionic liquids (ILs): 1,3-dimethylimidazolium methylphosphonate [DIMIM][(MeO)(H)PO2] and 1-ethyl-3-methylimidazolium methylphoshonate [EMIM][(MeO)(H)PO2]. The chemical modification of cellulose occurred through a transesterification reaction between the methyl phosphonate function of ILs and the primary alcohol functions of cellulose. The resulting cellulose structure and the amount of grafted phosphorus were then investigated by X-ray diffraction, ICP-AES, and ¹³C and ³¹P NMR spectroscopy. Depending on the IL type and initial cotton / IL ratio in the solution, regenerated cellulose contained up to 4.5% of phosphorus. The rheological behavior of cotton cellulose/ILs solutions and the microscale fire performances of modified cellulose were studied in order to ultimately prepare flame retardant cellulosic materials. Significant improvement in the flame retardancy of regenerated cellulose was obtained with a reduction of THR values down to about 5-6 kJ/g and an increase of char up to about 35 wt%.

| S-EPMC7181116 | biostudies-literature

Polymerizable Choline- and Imidazolium-Based Ionic Liquids Reinforced with Bacterial Cellulose for 3D-Printing.

Project description:In this work, a novel approach is demonstrated for 3D-printing of bacterial cellulose (BC) reinforced UV-curable ion gels using two-component solvents based on 1-butyl-3-methylimidazolium chloride or choline chloride combined with acrylic acid. Preservation of cellulose's crystalline and nanofibrous structure is demonstrated using wide-angle X-ray diffraction (WAXD) and atomic force microscopy (AFM). Rheological measurements reveal that cholinium-based systems, in comparison with imidazolium-based ones, are characterised with lower viscosity at low shear rates and improved stability against phase separation at high shear rates. Grafting of poly(acrylic acid) onto the surfaces of cellulose nanofibers during UV-induced polymerization of acrylic acid results in higher elongation at break for choline chloride-based compositions: 175% in comparison with 94% for imidazolium-based systems as well as enhanced mechanical properties in compression mode. As a result, cholinium-based BC ion gels containing acrylic acid can be considered as more suitable for 3D-printing of objects with improved mechanical properties due to increased dispersion stability and filler/matrix interaction.

| S-EPMC8471885 | biostudies-literature

Novel Ionic Conducting Composite Membrane Based on Polymerizable Ionic Liquids.

Project description:In this work, the design and characterization of new supported ionic liquid membranes, as medium-temperature polymer electrolyte membranes for fuel-cell application, are described. These membranes were elaborated by the impregnation of porous polyimide Matrimid® with different synthesized protic ionic liquids containing polymerizable vinyl, allyl, or methacrylate groups. The ionic liquid polymerization was optimized in terms of the nature of the used (photo)initiator, its quantity, and reaction duration. The mechanical and thermal properties, as well as the proton conductivities of the supported ionic liquid membranes were analyzed in dynamic and static modes, as a function of the chemical structure of the protic ionic liquid. The obtained membranes were found to be flexible with Young's modulus and elongation at break values were equal to 1371 MPa and 271%, respectively. Besides, these membranes exhibited high thermal stability with initial decomposition temperatures > 300 °C. In addition, the resulting supported membranes possessed good proton conductivity over a wide temperature range (from 30 to 150 °C). For example, the three-component Matrimid®/vinylimidazolium/polyvinylimidazolium trifluoromethane sulfonate membrane showed the highest proton conductivity-~5 × 10-2 mS/cm and ~0.1 mS/cm at 100 °C and 150 °C, respectively. This result makes the obtained membranes attractive for medium-temperature fuel-cell application.

| S-EPMC8588533 | biostudies-literature

Solubility Studies of Cyclosporine Using Ionic Liquids.

Project description:Six ionic liquids (ILs) were selected based on their chemical and physical properties to study the solubility of cyclosporine A. Of these, cyclosporine exhibited higher room temperature solubility in 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]) than in acetone, an effective molecular solvent used to solubilize and purify cyclosporine. The solubility of cyclosporine in the ILs dramatically increased at higher temperatures, a critical factor that cannot be varied in a wide range with low boiling molecular solvents. The differences in solubility were explored for cyclosporine purification. Cyclosporine was purified up to ∼93% with n-butylammonium acetate ([C4NH3][OAc]) and could be further purified to 95% using an IL/organic solvent biphasic system. After purification, cyclosporine was recovered as an amorphous solid using the ILs.

| S-EPMC6649182 | biostudies-literature