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Implementation of therapeutic in vivo gene editing using CRISPR/Cas relies on potent delivery of gene editing tools. Administration of ribonucleoprotein (RNP) complexes consisting of Cas protein and single guide RNA (sgRNA) offers short-lived editing activity and safety advantages over conventional viral and non-viral gene and RNA delivery approaches. By engineering lentivirus-derived nanoparticles (LVNPs) to facilitate RNP delivery, we demonstrate effective administration of SpCas9 as well as SpCas9-derived base and prime editors (BE/PE) leading to gene editing in recipient cells. Unique Gag/GagPol protein fusion strategies facilitate RNP packaging in LVNPs, and refinement of LVNP stoichiometry supports optimized LVNP yield and incorporation of therapeutic payload. We demonstrate near instantaneous target DNA cleavage and complete RNP turnover within 4 days. As a result, LVNPs provide high on-target DNA cleavage and lower levels of off-target cleavage activity compared to standard RNP nucleofection in cultured cells. LVNPs accommodate BE/sgRNA and PE/epegRNA RNPs leading to base editing with reduced bystander editing and prime editing without detectable indel formation. Notably, in the mouse eye, we provide the first proof-of-concept for LVNP-directed in vivo gene disruption. Our findings establish LVNPs as promising vehicles for delivery of RNPs facilitating donor-free base and prime editing without formation of double-stranded DNA breaks.

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The frontline therapy R-CHOP for patients with diffuse large B-cell lymphoma (DLBCL) has remained unchanged for two decades despite numerous Phase III clinical trials investigating new alternatives. Multiple large studies have uncovered genetic subtypes of DLBCL enabling a targeted approach. To further pave the way for precision oncology, we perform genome-wide CRISPR screening to uncover the cellular response to one of the components of R-CHOP, vincristine, in the DLBCL cell line SU-DHL-5. We discover important pathways and subnetworks using gene-set enrichment analysis and protein-protein interaction networks and identify genes related to mitotic spindle organization that are essential during vincristine treatment. The inhibition of KIF18A, a mediator of chromosome alignment, using the small molecule inhibitor BTB-1 causes complete cell death in a synergistic manner when administered together with vincristine. We also identify the genes KIF18B and USP28 of which CRISPR/Cas9-directed knockout induces vincristine resistance across two DLBCL cell lines. Mechanistic studies show that lack of KIF18B or USP28 counteracts a vincristine-induced p53 response suggesting that resistance to vincristine has origin in the mitotic surveillance pathway (USP28-53BP1-p53). Collectively, our CRISPR screening data uncover potential drug targets and mechanisms behind vincristine resistance, which may support the development of future drug regimens.

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Locus-directed DNA cleavage induced by the CRISPR-Cas9 system triggers DNA repair mechanisms allowing gene repair or targeted insertion of foreign DNA. For gene insertion to be successful, availability of a homologous donor template needs to be timed with cleavage of the DNA by the Cas9 endonuclease guided by a target-specific single guide RNA (sgRNA). We present a novel approach for targeted gene insertion based on a single integrase-defective lentiviral vector (IDLV) carrying a Cas9 off switch. Gene insertion using this approach benefits from transposon-based stable Cas9 expression, which is switched off by excision-only transposase protein co-delivered in IDLV particles carrying a combined sgRNA/donor vector. This one-vector approach supports potent (up to >80%) knockin of a full-length EGFP gene sequence. This traceless cell engineering method benefits from high stable levels of Cas9, timed intracellular availability of the molecular tools, and a built-in feature to turn off Cas9 expression after DNA cleavage. The simple technique is based on transduction with a single IDLV, which holds the capacity to transfer larger donor templates, allowing robust gene knockin or tagging of genes in a single step.

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We observe monopole oscillations in a mixture of Bose-Einstein condensates, where the usually dominant mean-field interactions are canceled. In this case, the system is governed by the next-order Lee-Huang-Yang (LHY) correction to the ground state energy, which describes the effect of quantum fluctuations. Experimentally such a LHY fluid is realized by controlling the atom numbers and interaction strengths in a ^{39}K spin mixture confined in a spherical trap potential. We measure the monopole oscillation frequency as a function of the LHY interaction strength as proposed recently by Jrgensen et al. [Phys. Rev. Lett. 121, 173403 (2018)PRLTAO0031-900710.1103/PhysRevLett.121.173403] and find excellent agreement with simulations of the complete experiment including the excitation procedure and inelastic losses. This confirms that the system and its collective behavior are initially dominated by LHY interactions. Moreover, the monopole oscillation frequency is found to be stable against variations of the involved scattering lengths in a broad region around the ideal values, confirming the stabilizing effect of the LHY interaction. These results pave the way for using the nonlinearity provided by the LHY term in quantum simulation experiments and for investigations beyond the LHY regime.

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Real-time monitoring of bioprocesses plays a key-role in modern industries, providing new information on full-scale production, thus enabling control of the process and allowing it to run at optimal conditions while minimizing waste. Monitoring of phosphates and ammonium in fermentation processes has a twofold interest: they are important nutrients for living organisms while at the same time constituting environmental nutrient pollutants, for which unnecessary use and disposal must be avoided. In this report, the possibility of simultaneous analysis of phosphates and ammonium in fermentations was verified using spectroscopy-based methods combined with chemometrics to construct calibration models. To achieve this, the models were based on synthetic samples mimicking real fermentation media, providing a dataset where the analytes were completely uncorrelated. Different at-line techniques (mid- and near- infrared spectroscopy, MIR and NIR) were evaluated for their ability to monitor quickly both analytes, in a wide range of concentrations (10-100 mM), in three media of different complexities. Partial Least Squares (PLS) models on MIR spectroscopy gave very good results, with prediction errors lower than 5 % for both analytes in all datasets. In contrast, the results for PLS models on NIR spectroscopy were inferior (prediction errors between 3 and 26 %) for both analytes, as, in the case of phosphate, it could be demonstrated that the model was based on based on indirect predictions.

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The ever-growing competition among global biotech industries has led to high demands on production consistency. A statistical strategy of performance mapping for production optimization is therefore of great economic significance. Process analytical technology (PAT)-based sensors such as mid-infrared (MIR) spectroscopy enable process monitoring through substrate and by-product concentrations that directly represent the physiology of cells. Combined with multivariate statistics, MIR can be employed as a strategy for production performance mapping. This study describes the use of at-line spectroscopy, chemometric modeling, and post-process fitting to characterize Lactobacillus acidophilus fermentations. The emphasis is on alternative arrangements of the data and chemometric methods principle component analysis (PCA), multivariate curve resolution (MCR), and parallel factor analysis (PARAFAC). Two key parameters, rate constant and time of inflection, are extracted by post-process fitting on the outcomes of these different models. Their use as process performance descriptors to characterize the dynamics of substrate consumption, product formation and batch-to-batch variations is suggested. The unconstrained PCA primarily described biomass change, while the constrained models PARAFAC and MCR (both the augmented and individual-run configurations) could model the decrease in sugars and increase in lactic acid over time. It was concluded that MCR on individual batch data, followed by post-process fitting, is the preferred strategy for MIR spectroscopic monitoring.

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Different opportunities are explored to evaluate quality variation in raw materials from biological origin. Assessment of raw materials attributes is an important step in a bio-based production as fluctuations in quality are a major source of process disturbance. This can be due to a variety of biological, seasonal, and supply scarcity reasons. The final properties of a product are invariably linked with the initial properties of the raw material. Thus, the operational conditions of a process can be tuned to drive the product to the required specification based on the quality assessment of the raw material being processed. Process analytical technology tools which enable this assessment in a far more informative and rapid manner than current industrial practices that rely on rule-of-thumb decisions are assessed. An example with citrus peels is used to demonstrate the conceptual and performance differences of distinct quality assessment approaches. The analysis demonstrates the advantage of characterization through multivariate data analysis coupled with a complementary spectroscopic technique, near-infrared spectroscopy. The quantitative comparative analysis of three different approaches, discriminant classification based on expert-knowledge, unsupervised classification, and spectroscopic correlation with reference physicochemical variables, is performed in the same dataset context. © 2018 Her Majesty the Queen in Right of Canada © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2762, 2019.

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AIM: Necrotising enterocolitis (NEC) is often staged according to Bell's 1978 system, but today's NEC cases are more immature than the ones that were used to develop Bell's stages. Our aim was to explore the clinical and radiographic findings of contemporary cases of NEC and spontaneous intestinal perforation. METHODS: We coded the clinical records of all cases of NEC stages I-III and spontaneous intestinal perforation born in 2006-2015 at the tertiary department of neonatology at Rigshospitalet, Denmark, for 16 clinical and radiographic symptoms and signs at disease onset and at climax. These variables were explored using principal component analysis, which can detect patterns in large datasets. RESULTS: We reviewed 640 clinical records and included 158 cases of NEC or spontaneous intestinal perforation. When we entered the clinical and radiographic signs at disease climax, the cases were roughly grouped according to Bell's stages, except for a small group of NEC III cases, who were grouped with the cases of spontaneous intestinal perforation. CONCLUSION: An analysis of the pattern of clinical and radiographic findings in a 2006-2015 population of NEC cases supported Bell's 1978 staging system. However, the separation between NEC and spontaneous intestinal perforation still poses a difficult task.

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In this study, the aim was to establish if loss of DNA integrity is a cause of loss of culturability for probiotic bacteria during storage in dry state. The number of colony forming units (CFU), number of metabolically active cells, and DNA integrity during dry storage of probiotic strains, B. animalis subsp. lactis BB-12 and L. acidophilus LA-5, were investigated. The probiotic strains were freeze-dried and stored at 20°C, with and without oxygen present, and at water activity levels 0.22 or 0.32. Dry storage resulted in a decrease in CFU during the entire storage period. The number of metabolically active cells was unchanged during storage of B. animalis subsp. lactis BB-12, but did decrease during the first week of storage of L. acidophilus LA-5. Loss of DNA integrity was evident for both strains during storage and correlated well with the loss of CFU. Both loss of CFU and loss of DNA integrity were significantly greater for both strains when oxygen was present and when aw was increased. Statistical analysis indicates a possible causal relationship between DNA degradation and loss of culturability and this idea is consistent with the function of DNA at cell division. The study contributes with new knowledge of the cause for loss of CFU during dry storage of probiotic bacteria, which possibly can aid in the improvement of preservation techniques. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:231-242, 2018.

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Protein hydrolysates are of great interest in the food industry due to their nutritional and functional properties, but their use often implies solubilization in water and therefore hamper the use of plant proteins with inherent low water solubility. Protein solubility in water can be modified by enzymatic hydrolysis, but during this process several collateral properties of the protein hydrolysates changes. It is therefore important to determine the end-point of the process and to monitor its development. In this feasibility study, we demonstrated the potential of different spectroscopic techniques (1H NMR and IR) coupled with chemometrics analysis in monitoring the hydrolysis of five different industrial grade plant proteins by the enzyme Alcalase. Logarithmic modeling of the PCA (Principal Component Analysis) scores confirmed that they can represent a measurement of the solubilized protein material released and resulted in kinetic parameters describing the suitability of protein sources as substrates for the hydrolysis. This way, we showed that a qualitative evaluation of the degree of hydrolysis is possible using fast at-line technologies and PCA.

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An industrial scale biomass production using batch or fed-batch fermentations usually optimized by selection of bacterial strains, tuning fermentation media, feeding strategy, and temperature. However, in-depth investigation of the biomass metabolome during the production may reveal new knowledge for better optimization. In this study, for the first time, the authors investigated seven fermentation batches performed on five Streptoccoccus thermophilus strains during the biomass production at Chr. Hansen (Denmark) in a real life large scale fermentation process. The study is designed to investigate effects of batch fermentation, fermentation time, production line, and yeast extract brands on the biomass metabolome using untargeted GC-MS metabolomics. Processing of the raw GC-MS data using PARAFAC2 revealed a total of 90 metabolites out of which 64 are identified. Partitioning of the data variance according to the experimental design was performed using ASCA and revealed that batch and fermentation time effects and their interaction term were the most significant effects. The yeast extract brand had a smaller impact on the biomass metabolome, while the production line showed no effect. This study shows that in-depth metabolic analysis of fermentation broth provides a new tool for advanced optimization of high-volume-low-cost biomass production by lowering the cost, increase the yield, and augment the product quality.

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SCOPE: The aim of the paper is to investigate whether changes in the metabolome could explain observed changes in body composition in overweight adults after consumption of butter with high level of medium-chain fatty acids (MCFAs) in combination with casein or whey. METHODS AND RESULTS: With GC-TOF and LC-Q/MS, metabolites in plasma and urine from a 12-week randomized double-blinded human intervention including 52-abdominally overweight adults were analyzed. The participants consumed 63 g per day of milk fat (high or low in MCFAs) and 60 g per day of protein (whey or casein). Urinary loss of the tricarboxylic acid cycle metabolites and a concomitantly increase of glycerol in blood were observed in the whey + high-MCFAs group, indicating potential lower anabolic processes, such as lipogenesis, by draining substrates. High intake of MCFAs resulted in elevated level of urinary adipic (independently of protein type) and plasma sebacic acid (with whey), indicating a potential increase in oxidation of MCFAs, which might lead to energy loss. CONCLUSION: The type of protein showed highest effect on the overall metabolic profiles, but ω-oxidation of MCFAs in the liver seemed to be the main reason for the observed reduction in body fat mass after consumption of high MCFAs, independent of type of protein.

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Fluorescence spectroscopy is a sensitive and selective technique, which can be of great value in bioprocesses to provide online, real-time measures of chemical compounds. Although fluorescence spectroscopy is a widely studied method, not much attention has been given to issues concerning intensity variations in the fluorescence landscapes due to pH fluctuations. This study elucidates how pH fluctuations cause intensity changes in fluorescence measurements and thereby decreases the quality of the subsequent quantification. A photo-degradation process of riboflavin was investigated by fluorescence spectroscopy and used as a model system. A two-step modeling approach, combining weighted PARAllel FACtor analysis (PARAFAC) with weighted non-linear regression of the known reaction kinetics, is suggested as a way of handling the fluorescence intensity shifts caused by the pH changes. The suggested strategy makes it possible to compensate for uncertainties in the shifted data and thereby obtain more reliable concentration profiles for the chemical compounds and kinetic parameters of the reaction.

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Lactic acid bacteria with antifungal properties are applied for biopreservation of food. In order to further our understanding of their antifungal mechanism, there is an ongoing search for bioactive molecules. With a focus on the metabolites formed, bioassay-guided fractionation and comprehensive screening have identified compounds as antifungal. Although these are active, the compounds have been found in concentrations that are too low to account for the observed antifungal effect. It has been hypothesized that the formation of metabolites and consumption of nutrients during bacterial fermentations form the basis for the antifungal effect, i.e., the composition of the exometabolome. To build a more comprehensive view of the chemical changes induced by bacterial fermentation and the effects on mold growth, a strategy for correlating the exometabolomic profiles with mold growth was applied. The antifungal properties were assessed by measuring mold growth of two Penicillium strains on cell-free ferments of three strains of Lactobacillus paracasei pre-fermented in a chemically defined medium. Exometabolomic profiling was performed by reversed-phase liquid chromatography in combination with mass spectrometry in electrospray positive and negative modes. By multivariate data analysis, the three strains of Lb. paracasei were readily distinguished by the relative difference of their exometabolomes. The relative differences correlated with the relative growth of the two Penicillium strains. Metabolic footprinting proved to be a supplement to bioassay-guided fractionation for investigation of antifungal properties of bacterial ferments. Additionally, three previously identified and three novel antifungal metabolites from Lb. paracasei and their potential precursors were detected and assigned using the strategy.

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A novel biosensor for detecting DNA damage induced by benzo(a)pyrene (BP) and its metabolite was presented in this work. The nafion-solubilized single wall carbon nanotubes-ionic liquid (SWCNTs-NA-IL) composite film was prepared and then horseradish peroxidase (HRP) and double-stranded DNA were alternately assembled on the composite film by the layer-by-layer method. The biosensor was characterized by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), differential pulse voltammetry (DPV), scanning electron microscopy (SEM) and computational methods. UV-vis spectrophotometry was also used to investigate DNA damage induced by BP and its metabolites in solution. The DNA biosensor was treated separately in BP, hydrogen peroxide (H2O2) and in their mixture, respectively. The EIS analysis showed a decrease in the charge transfer resistance at the DNA/HRP/SWCNTs-NA-IL/GCE incubated in a mixture of HRP and H2O2, because HRP in the presence of H2O2 could mimic enzymatic effects of cytochrome P450 (CYP450) to metabolize BP which could cause significant DNA damage and the exposed DNA bases reduced the electrostatic repulsion of the negatively charged redox probe and leads to Faradaic impedance changes. Finally, a novel biosensor for BP determination was developed and this method provided an indirect, and quantitative estimation of DNA damage in vitro.

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For the first time, several second-order calibration models based on artificial neural network-residual bilinearization (ANN-RBL), unfolded-partial least squares-RBL (U-PLS/RBL), multidimensional-partial least squares-RBL (N-PLS/RBL), multivariate curve resolution-alternating least squares (MCR-ALS), and parallel factor analysis 2 (PARAFAC2) were used to exploiting second-order advantage to identify which technique offers the best predictions for the simultaneous quantification of norepinephrine (NE), paracetamol (AC), and uric acid (UA) in the presence of pteroylglutamic acid (FA) as an uncalibrated interference at an electrochemically oxidized glassy carbon electrode (OGCE). Three-way differential pulse voltammetric (DPV) arrays were obtained by recording the DPV signals at different pulse heights. The recorded three-way arrays were both non-bilinear and non-trilinear therefore, the observed shifts in the recorded DPV data were corrected using correlation optimised warping (COW) algorithm. All the algorithms achieved the second-order advantage and were in principle able to overcome the problem of the presence of unexpected interference. Comparison of the performance of the applied second-order chemometric algorithms confirmed the more superiority of U-PLS/RBL to resolve complex systems. The results of applying U-PLS/RBL for the simultaneous quantification of the studied analytes in human serum samples were also encouraging.

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For the first time, an analytical methodology based on differential pulse voltammetry (DPV) at a glassy carbon electrode (GCE) and integration of three efficient strategies including variable selection based on ant colony optimization (ACO), mathematical pre-processing selection by genetic algorithm (GA), and sample selection (SS) through a distance-based procedure to improve partial least squares-1 (PLS-1, ACO-GA-SS-PLS-1) multivariate calibration (MVC) for the simultaneous determination of five opium alkaloids including morphine (MOP), noscapine (NOP), thebaine (TEB), codeine (COD), and papaverine (PAP) was used and validated. The baselines of the DPV signals were modeled as a smooth curve, using P-splines, a combination of B-splines and a discrete roughness penalty. After subtraction of the baseline we got a signal with a two-component probability density. One component was for the peaks and it was approximated by a uniform distribution on the potential axis. The other component was for the observed noise around the baseline. Some sources of bi-linearity deviation for electrochemical data were discussed and analyzed. The lack of bi-linearity was tackled by potential shift correction using correlation optimized warping (COW) algorithm. The MVC model was developed as a quinternary calibration model in a blank human serum sample (drug-free) provided by a healthy volunteer to regard the presence of a strong matrix effect which may be caused by the possible interferents present in the serum, and it was validated and tested with two independent sets of analytes mixtures in the blank and actual human serum samples, respectively. Fortunately, the proposed methodology was successful in simultaneous determination of MOP, NOP, TEB, COD, and PAP in both blank and actual human serum samples and its results were satisfactory comparable to those obtained by applying the reference method based on high performance liquid chromatography-ultraviolet detection (HPLC-UV).

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In this study, a novel biosensing system for the determination of biotin (BTN) based on electrodeposition of palladium-iron-nickel (PdFeNi) trimetallic alloy nanoparticles (NPs) onto a glassy carbon electrode (GCE) modified with a room-temperature ionic liquid (RTIL)-chitin (Ch) composite film (PdFeNi/ChRTIL/GCE) is established. NPs have a wide range of applications in science and technology and their sizes are often measured using transmission electron microscopy (TEM) or X-ray diffraction. Here, we used a pattern recognition method (digital image processing, DIP) for measuring particle size distributions (PSDs) from scanning electron microscopic (SEM) images in the presence of an uneven background. Different depositions were performed by varying the number of cyclic potential scans (N) during electroreduction step. It was observed that the physicochemical properties of the deposits were correlated to the performance of the PdFeNi/ChRTIL/GCE with respect to BTN assay. The best results were obtained for eight electrodeposition cyclic scans, where small-sized particles (19.54 ± 6.27 nm) with high density (682 particles µm(-2)) were obtained. Under optimized conditions, a linear range from 2.0 to 44.0 × 10(-9) mol L(-1) and a limit of detection (LOD) of 0.6 × 10(-9) mol L(-1) were obtained. The PdFeNi/ChRTIL nanocomposite showed excellent compatibility, enhanced electron transfer kinetics, large electroactive surface area, and was highly sensitive, selective, and stable toward BTN determination. Finally, the PdFeNi/ChRTIL/GCE was satisfactorily applied to the determination of BTN in infant milk powder, liver, and egg yolk samples.

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For the first time, interaction of vitamin B7 (VB7) with bovine serum albumin (BSA) was investigated with the aim of developing a method for the analysis of BSA. The interaction of VB7 with BSA was investigated by cyclic voltammetry (CV), linear sweep voltammetry (LSV), and differential pulse voltammetry (DPV) at a multi-walled carbon nanotubes-modified glassy carbon electrode (MWCNTs/GCE). The recorded electrochemical data was combined with UVvis and fluorescence (F) spectroscopic data into a row- and column-wise augmented matrix and resolved by multivariate curve resolution-alternating least squares (MCR-ALS) as an efficient chemometric tool, and this assisted in the further elucidation of the above interaction. Also, with aid of MCR-BANDS method, the absence of rotational ambiguity was verified in the obtained results and we confirmed that the obtained results were unambiguous and reliable. The binding of VB7 to BSA was also modeled by molecular docking methods. Excellent agreement was found between the experimental and computational results. The differences of DPV responses of VB7 in the absence and presence of BSA (ΔI) were found to be linearly related to BSA concentration between 0.5×10(-9) mol L(-1) and 35.0×10(-9) mol L(-1), and a limit of detection (LOD, 3Sb/b) of 0.22×10(-9) mol L(-1) was calculated. Finally, the DPV method was further applied to the determination of serum albumin (SA) in serum samples obtained from Holstein cows and the results were in good agreement with those obtained by a medical diagnostic laboratory whose method was based on traditional cellulose acetate electrophoresis. The MWCNTs/GCE showed enhanced electron transfer kinetics, large electroactive surface area, and was highly sensitive, selective, and stable towards SA determination. The satisfactory analytical performance of the proposed method would make it potentially advantageous for a broad range of biosensing and clinical applications.

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A computationally engineered impedimetric naltrexone (NLT) biosensor based on immobilization of bovine serum albumin (BSA) onto fullerene-C60/glassy carbon electrode (FLR/GCE) has been developed using initial characterization by computational methods and complementing them by experimental ones. Computational results showed that BSA hydrophobically binds to FLR which is energetically favorable and leads to the spontaneous formation of the stable nanobiocomposite and also showed that interaction of NLT with BSA is mainly driven by hydrogen bonding and hydrophobic interactions. Besides complementing the computational studies, experimental results showed that addition of FLR to the surface of the electrode facilitated electron transfer reactions, and also showed that the presence of BSA inhibits the interfacial electron transfer in some extent due to the non-conductive properties of BSA. The presence of NLT may form a negatively charged electroactive complex with BSA which repels the negatively charged redox probe and decelerates interfacial electron transfer leading to obvious faradaic impedance change. The faradaic impedance responses were linearly related to naltrexone concentration between 0.1 nM and 80 nM and limit of detection (LOD) was calculated to be 0.01 nM 3Sb/b. Finally, the proposed biosensor was successfully applied to determination of NLT in urine samples of both healthy and addict volunteers.

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