A novel FRET approach for in situ investigation of cellulase–cellulose interaction

A novel real-time in situ detection method for the investigation of cellulase–cellulose interactions based on fluorescence resonance energy transfer (FRET) has been developed. FRET has been widely used in biological and biophysical fields for studies related to proteins, nucleic acids, and small biological molecules. Here, we report the efficient labeling of carboxymethyl cellulose (CMC) with donor dye 5-(aminomethyl)fluorescein and its use as a donor in a FRET assay together with an Alexa Fluor 594 (AF594, acceptor)–cellulase conjugate as acceptor. This methodology was successfully employed to investigate the temperature dependency of cellulase binding to cellulose at a molecular level by monitoring the fluorescence emission change of donor (or acceptor) in a homogeneous liquid environment. It also provides a sound base for ongoing cellulase–cellulose study using cellulosic fiber.     

Rolling cycle amplification based single-color quantum dots–ruthenium complex assembling dyads for homogeneous and highly selective detection of DNA

In this work, a new, label-free, homogeneous, highly sensitive, and selective fluorescent biosensor for DNA detection is developed by using rolling-circle amplification (RCA) based single-color quantum dots–ruthenium complex (QDs–Ru) assembling dyads. This strategy includes three steps: (1) the target DNA initiates RCA reaction and generates linear RCA products; (2) the complementary DNA hybridizes with the RCA products to form long double-strand DNA (dsDNA); (3) [Ru(phen)₂(dppx)]²⁺ (dppx = 7,8-dimethyldipyrido [3,2-a:2′,3′-c] phenanthroline) intercalates into the long dsDNA with strong fluorescence emission. Due to its strong binding propensity with the long dsDNA, [Ru(phen)₂(dppx)]²⁺ is removed from the surface of the QDs, resulting in restoring the fluorescence of the QDs, which has been quenched by [Ru(phen)₂(dppx)]²⁺ through a photoinduced electron transfer process and is overlaid with the fluorescence of dsDNA bonded Ru(II) polypyridyl complex (Ru-dsDNA). Thus, high fluorescence intensity is observed, and is related to the concentration of target. This sensor exhibits not only high sensitivity for hepatitis B virus (HBV) ssDNA with a low detection limit (0.5 pM), but also excellent selectivity in the complex matrix. Moreover, this strategy applies QDs–Ru assembling dyads to the detection of single-strand DNA (ssDNA) without any functionalization and separation techniques.     

Magnetic nanomaterial–based electrochemical biosensors for the detection of diverse circulating cancer biomarkers

Electrochemical biosensors are highly compatible with modern advancements in magnetic nanomaterials. In particular, the versatile nature of magnetic nanomaterials as a universal platform for selective isolation of diverse forms of cancer biomarkers in body circulation, is highly synergistic with electrochemical biosensors for elevating biosensing performance to unprecedented levels. Such diverse circulating target biomolecules include cell surface proteins of circulating tumor cells and extracellular vesicles (EVs), as well as circulating tumor nucleic acids (i.e. ctDNA/ctRNA). This focussed review serves to discuss the latest work in the fields of magnetic nanomaterials and electrochemistry to tackle existing analysis challenges of diverse circulating biomarkers in cancer.     

Liquid chromatography–tandem mass spectrometry method for the detection of marine lipophilic toxins under alkaline conditions

A new LC–MS/MS method for the separation and detection of the most prominent marine lipophilic toxin groups comprising okadaic acid, dinophysistoxins, yessotoxins, azaspiracids, pectenotoxins, spirolides and some okadaic acid fatty acid esters has been developed. With this method 28 different marine lipophilic biotoxins can be analysed in a single run. Separation was achieved with an acetonitrile/water gradient containing ammonium hydroxide (pH 11). All toxins were stable under these basic conditions. Compared to chromatography using an acidic gradient, the limit of detection (LODs) for okadaic acid, yessotoxin, gymnodimine and 13-desmethyl spirolide C were improved two- to three-fold, mainly due to better peak shapes. The azaspiracids and pectenotoxins-2 showed comparable LODs under acidic and basic conditions. A major advantage of the developed method is that toxins can be clustered in retention time windows separated for positively and negatively ionized molecular ions. Therefore, there is no need for rapid polarity switching or two separate runs for one sample. The new method showed good repeatability and reproducibility and is an important step in the development of alternatives to the animal tests currently in use for shellfish toxin analysis.     

A qualitative/quantitative approach for the detection of 37 tryptamine-derived designer drugs, 5 β-carbolines, ibogaine, and yohimbine in human urine and plasma using standard urine screening and multi-analyte approaches

The first synthetic tryptamines have entered the designer drug market in the late 1990s and were distributed as psychedelic recreational drugs. In the meantime, several analogs have been brought onto the market indicating a growing interest in this drug class. So far, only scarce analytical data were available on the detectability of tryptamines in human biosamples. Therefore, the aim of the presented study was the development and full validation of a method for their detection in human urine and plasma and their quantification in human plasma. The liquid chromatography-linear ion trap mass spectrometry method presented covered 37 tryptamines as well as five β-carbolines, ibogaine, and yohimbine. Compounds were analyzed after protein precipitation of urine or fast liquid–liquid extraction of plasma using an LXQ linear ion trap coupled to an Accela ultra ultra high-performance liquid chromatography system. Data mining was performed via information-dependent acquisition or targeted product ion scan mode with positive electrospray ionization. The assay was selective for all tested substances with limits of detection in urine between 10 and 100 ng/mL and in plasma between 1 and 100 ng/mL. A validated quantification in plasma according to international recommendation could be demonstrated for 33 out of 44 analytes.     

Development and validation of a method for the detection and confirmation of biomarkers of exposure in human urine by means of restricted access material-liquid chromatography–tandem mass spectrometry

The present article describes the development and validation of a LC–MS/MS method for the determination and confirmation of biomarkers of exposure to different types of xenobiotics in human urine. The method combines the use of a restricted access material (RAM) coupled on-line to a LC–IT-MS system; in this way, a rapid and efficient matrix cleanup was achieved, reducing manual sample preparation to freezing and sample filtration. The ion trap (IT) mass spectrometry detector provided the selectivity, sensitivity and ruggedness needed for confirmatory purposes. The on-line RAM-LC–MS/MS method developed here has been validated as a quantitative confirmatory method according to the European Union (EU) Decision 2002/657/EC. The validation steps included the verification of linearity, repeatability, specificity, trueness/recovery, reproducibility, stability and ruggedness in fortified urine samples. Repeatability and within-laboratory reproducibility, measured as intraday and interday precisions, were evaluated at two concentration levels, being 12.7% or below at the concentration corresponding to the quantification limits. Matrix effects and non-targeted qualitative analyses were also evaluated in fortified urine samples. Decision limits (CC_α) and detection capabilities (CC_β) were in the range of 3.6–16.5 and 6.0–28.1 ng mL⁻¹ respectively. The results of the validation process revealed that the proposed method is suitable for reliable quantification and confirmation of biomarkers of exposure to xenobiotics in human urine at low ng mL⁻¹ levels. In addition, working in Data-Dependent Scan mode the proposed method can be used for the screening of these compounds in urine samples.     

pH-controlled dispersive liquid–liquid microextraction for the analysis of ionisable compounds in complex matrices: Case study of ochratoxin A in cereals

A new sample preparation procedure, termed pH-controlled dispersive liquid–liquid microextraction (pH-DLLME), has been developed for the analysis of ionisable compounds in highly complex matrices. This DLLME mode, intended to improve the selectivity and to expand the application range of DLLME, is based on two successive DLLMEs conducted at opposite pH values. pH-DLLME was applied to determination of ochratoxin A (OTA) in cereals. The hydrophobic matrix interferences in the raw methanol extract (disperser, 1 mL) were removed by a first DLLME (I DLLME) performed at pH 8 to reduce the solubility of OTA in the extractant (CCl₄, 400 μL). The pH of the aqueous phase was then adjusted to 2, and the analyte was extracted and concentrated by a second DLLME (extractant, 150 μL C₂H₄Br₂). The main factors influencing the efficiency of pH-DLLME including type and volume of I DLLME extractant, as well as the parameters affecting the OTA extraction by II DLLME, were studied in detail. Under optimum conditions, the method has detection and quantification limits of 0.019 and 0.062 μg kg⁻¹, respectively, with OTA recoveries in the range of 81.2–90.1% (n = 3). The accuracy of the analytical procedure, evaluated with a reference material (cereal naturally contaminated with OTA), is acceptable (accuracy of 85.6% ± 1.7, n = 5).     

An in silico approach to design peptide mimetics based on docking and molecular dynamics simulation of EGFR–matuzumab complex

Epidermal growth factor receptor (EGFR) plays an essential role in anticancer therapy. Matuzumab is an antibody for the treatment of colorectal, lung and stomach cancer. Matuzumab binds efficiently to EGFR and blocks its phosphorylation. The recent clinical successes have established application of peptides for cancer treatment. The present contribution introduces an in silico approach to design peptides based on molecular dynamics simulation (MDs) of the matuzumab-EGFR complex in water environment. Moreover, principal component analysis has been used to select multiple conformations of the complex in MDs for designing the peptides. The paratope and epitope in each conformation of the complex were determined, and the alanine scanning was used to identify the hot spots of EGFR conformers. The conformations of the peptides were optimized using PEP-FOLD server and MDs. The selected conformations were analyzed in a docking study to realize the binding site of the EGFR. Finally, pharmokinetics properties of the peptides were calculated. The designed oligopeptides were EWRSYYYWH, YYYWHNEWN, YYYWHNEWS and HNHSRNYGS with a higher affinity to the EGFR relative to the previously reported peptides. The newly designed peptides were investigated for their in vivo toxicities on rats, and all of them were non-toxic.     

Development of effervescence-assisted switchable polarity solvent homogeneous liquid-phase microextraction for the determination of permethrin and deltamethrin in water samples prior to gas chromatography–flame ionization detection

An effervescent tablet-assisted switchable polarity solvent–based homogeneous liquid-phase microextraction combined with gas chromatography with flame ionization detection has been conducted for the separation, preconcentration, and detection of permethrin and deltamethrin in the river water specimens. Triethylamine (TEA) was utilized as the switchable polarity solvent in this method. The switching process was carried out by the dissolution of an effervescent tablet including an effervescency agent (sodium carbonate) and a proton donor agent (citric acid). Changing the pH of the specimen solution enhanced the conversion of TEA into protonated triethylamine carbonate through the tablet that generated carbon dioxide bubbles in situ. Finally, the addition of sodium hydroxide changed the ionization state of TEA and separated the two phases. Influential factors in the extraction were investigated. According to optimal situations, the limit of detection and the limit of quantification were 0.16 and 0.5 μg L⁻¹ for permethrin and 0.03 and 0.1 μg L⁻¹ for deltamethrin, respectively. The preconcentration factor was 194 in river water samples and inter- and intra-day precision (relative standard deviation %; n = 5) was <5%. The extraction recovery was obtained in the range of 93.0%–97% for permethrin and deltamethrin in water samples.     

Development of a fast and selective method for the sensitive determination of anatoxin-a in lake waters using liquid chromatography–tandem mass spectrometry and phenylalanine-d 5 as internal standard

Anatoxin-a is a potent alkaloid neurotoxin produced by a number of cyanobacterial species and released in freshwaters during cyanobacterial blooms. Its high toxicity is responsible for several incidents of lethal intoxications of birds and mammals around the world; therefore anatoxin-a has to be regarded as a health risk and its concentration in lakes and water reservoirs should be monitored. Phenylalanine is a natural amino acid, also present in freshwaters, isobaric to anatoxin-a, with a very similar fragmentation pattern and LC retention. Since misidentification of phenylalanine as anatoxin-a has been reported in forensic investigations, special care must be taken in order to selectively determine traces of anatoxin-a in the presence of naturally occurring phenylalanine. A fast LC tandem MS method was developed by using a 1.8 μm 50 × 2.1 mm C18 column for the separation of anatoxin-a and phenylalanine, achieving a 3-min analysis time. Isotopically labelled phenylalanine-d ₅ was employed as internal standard to compensate for electrospray ion suppression and sample preconcentration losses. Both compounds were preconcentrated 1,000-fold on a porous graphitic carbon solid-phase extraction (SPE) cartridge after adjustment of sample pH to 10.5. The method was validated by using lake water spiked at four different levels from 0.01 to 1 μg L⁻¹. Anatoxin-a recovery ranged from 73 to 97%, intra-day precision (RSD%) ranged from 4.2 to 5.9, while inter-day precision (RSD%) ranged from 4.2 to 9.1%. Limits of detection and quantification were 0.65 and 1.96 ng L⁻¹ respectively. The method was successfully applied for the detection of anatoxin-a in Greek lakes at concentrations ranging from less than 0.6 to 9.1 ng L⁻¹.     

Review of HPLC–MS methods for the analysis of nicotine and its active metabolite cotinine in various biological matrices

In recent years, tobacco smoking is a risk factor for a series of diseases, including cardiovascular diseases, cerebrovascular diseases, and cancers. Nicotine, the primary component of tobacco smoke, is mainly transformed to its active metabolite cotinine, which is often used as a biomarker for tobacco exposure for its higher blood concentration and longer residence time than nicotine. Various analytical methods have been developed for the determination of nicotine and cotinine in biological matrices. This article reviewed the HPLC–MS based methods for nicotine and/or cotinine analysis in various biological matrices. The sample preparation, mass and chromatographic conditions, and method validation results of these methods have been summarized and analyzed. The sample was mainly pretreated by protein precipitation and/or extraction. Separation was achieved using methanol and/or acetonitrile:water (with or without ammonium acetate) on C18 columns and acetonitrile:water (with formic acid, ammonium acetate/formate) on HILIC columns. Nicotine-d3, nicotine-d4, and cotinine-d3 were commonly used internal standards (ISs). Other non-deuterated ISs such as ritonavir, N-ethylnorcotinine, and milrinone were also used. For both nicotine and cotinine, the calibration range was 0.005–35,000 ng/mL, the matrix effect was 75.96–126.8%, and the recovery was 53–124.5%. The two analytes were stable at room temperature for 1–10 days, at −80°C for up to 6 months, and after three to six freeze–thaw cycles. Comedications did not affect nicotine and cotinine analyses.     

Integrated biological–chemical approach for the isolation and selection of polyaromatic mutagens in surface waters

Many environmental mutagens, including polyaromatic compounds are present in surface waters, often in complex mixtures and at low concentrations. The present study provides and applies a novel, integrated approach to isolate polyaromatic mutagens in river water using a sample from the River Elbe. The sample was taken downstream of industrial discharges using blue rayon (BR) as a passive sampler that selectively adsorbs polyaromatic compounds and was subjected to effect-directed fractionation in order to characterise the compounds causing the detected effect(s). The procedure relies on three complementary fractionation steps, the Ames fluctuation assay with strains TA98, YG1024 and YG1041 with and without S9 activation and analytical screening. Several mutagenic fractions were isolated by combining mutagenicity testing with fractionation. The enhanced mutagenicity in the nitroreductase and/or O-acetyltransferase overexpressing strains YG1024 and YG1041 strains suggested amino- and/or nitro-compounds causing mutagenicity in several fractions. Analytical screening of mutagenic fractions with LC-HRMS/MS provided a list of molecular formulas typically containing one to ten nitrogen and at least two oxygen atoms supporting the presence of amino and nitro-compounds in the mutagenic fractions.

Development and validation of an LC–MS/MS method for the quantification of artificial sweeteners in human matrices

Artificial sweeteners are widely used as substitutes for sugar. The sweeteners are generally considered safe, however their whereabouts during pregnancy and lactation and the effect on child development are poorly explored. There is a need for new tools to measure these substances during pregnancy and lactation. Here, we describe the development and validation of a sensitive liquid chromatography–tandem mass spectrometry method for the simultaneous quantification of acesulfame, cyclamate, saccharin and sucralose in human plasma, umbilical cord blood, amniotic fluid and breast milk. The samples were prepared by protein precipitation and separated on a Luna Omega Polar C₁₈ column (2.1 × 50 mm, 1.6 μm). Electrospray ionization in negative mode and multiple reaction monitoring were used to monitor the ion transitions. The validated concentration ranges were from 1 to 500 ng/ml (10–500 ng/ml for sucralose). Interassay precisions were all ≤15% and the accuracies were within ±15%. Stability, linearity, dilution integrity, carryover and recovery were also examined and satisfied the validation criteria. Finally, this analytical method was successfully applied on spiked samples of plasma, umbilical cord blood, amniotic fluid and breast milk, proving its suitability for use in clinical studies on artificial sweeteners, including during pregnancy and lactation.     

Are luminescent bacteria suitable for online detection and monitoring of toxic compounds in drinking water and its sources?

Biosensors based on luminescent bacteria may be valuable tools to monitor the chemical quality and safety of surface and drinking water. In this review, an overview is presented of the recombinant strains available that harbour the bacterial luciferase genes luxCDABE, and which may be used in an online biosensor for water quality monitoring. Many bacterial strains have been described for the detection of a broad range of toxicity parameters, including DNA damage, protein damage, membrane damage, oxidative stress, organic pollutants, and heavy metals. Most lux strains have sensitivities with detection limits ranging from milligrams per litre to micrograms per litre, usually with higher sensitivities in compound-specific strains. Although the sensitivity of lux strains can be enhanced by various molecular manipulations, most reported detection thresholds are still too high to detect levels of individual contaminants as they occur nowadays in European drinking waters. However, lux strains sensing specific toxic effects have the advantage of being able to respond to mixtures of contaminants inducing the same effect, and thus could be used as a sensor for the sum effect, including the effect of compounds that are as yet not identified by chemical analysis. An evaluation of the suitability of lux strains for monitoring surface and drinking water is therefore provided.     

An approach to the Paal–Knorr pyrroles synthesis in the presence of β-cyclodextrin in aqueous media

An efficient and facile method for the synthesis of N-substituted pyrroles in moderate to good yields by the Paal–Knorr reaction of γ-diketones with amines in the presence of β-cyclodextrin in aqueous media has been developed.Moreover,this process tolerated diamines(e.g.,para-,meta- or orthophenylenediamine)to construct bis-pyrrole or mono-pyrrole derivates.β-Cyclodextrin can be recovered easily after the reactions and reused without evident loss in activity.     

Electrochemical approaches for the detection of amyloid-β, tau,and α-synuclein

According to the World Health Organization, there are 47 million people worldwide who are afflicted with dementia today, and this is expected to rise to 132 million by 2050. Therefore, it is pertinent to develop efficient analytical methods such as electrochemical biosensors to study these disorders and diagnose them early. This review highlights some of the recent key developments in the use of electrochemical biosensors to study the biomarkers related to neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease. Especially, we focus on the applications of electrochemistry to analyze amyloid-β and tau related to Alzheimer's disease and α-synuclein related to Parkinson's disease.