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Acetylcholinesterase is the main neurotransmitter in the cholinergic system. Impairment of the cholinergic system can be a reason for Alzheimer's and multiple sclerosis. Alzheimer's disease and multiple sclerosis affect patients and their relatives' daily lives enormously. New therapies with more benefits than current therapies for these diseases would facilitate patients' lives. In this respect, discovering novel acetylcholine esterase inhibitors with more effective and fewer side effects is highly important. Machine learning algorithms are very useful to predict the activity of molecules for a biological target. In this study, our classification models were built with Deep Neural Networks (DNN), Support Vector Machines (SVM), and Extreme Gradient Boosting (XGBoost) to predict molecules as active or inactive for acetylcholinesterase inhibitors. These models were evaluated with various metrics. As a result, The DNN model showed a better ability to classify (accuracy=0.93, F1 score=0.88, MCC=0.8, Roc-Auc=0.89 in the test set) molecules than the other models. [ABSTRACT FROM AUTHOR]

Photoelectron Photoion Coincidence (PEPICO) spectroscopy holds the promise of a universal, isomer-selective, and sensitive analytical technique for time-resolved quantitative analysis of bimolecular chemical reactions. Unfortunately, its low dynamic range of ~103 has largely precluded its use for this purpose, where a dynamic range of at least 105 is generally required. This limitation is due to the false coincidence background common to all coincidence experiments, especially at high count rates. Electron/ion pairs emanating from separate ionization events but arriving within the ion time of flight (TOF) range of interest constitute the false coincidence background. Although this background has uniform intensity at every m/z value, the Poisson scatter in the false coincidence background obscures small signals. In this paper, temporal ion deflection coupled with a position-sensitive ion detector enables suppression of the false coincidence background, increasing the dynamic range in the PEPICO TOF mass spectrum by 2-3 orders of magnitude. The ions experience a time-dependent electric deflection field at a well-defined fraction of their time of flight. This deflection defines an m/zand ionization-time dependent ion impact position for true coincidences, whereas false coincidences appear randomly outside this region and can be efficiently suppressed. When cold argon clusters are ionized, false coincidence suppression allows us to observe species up to Ar9+, whereas Ar9+ is the largest observable cluster under traditional operation. This advance provides mass-selected photoelectron spectra for fast, high sensitivity quantitative analysis of reacting systems. [ABSTRACT FROM AUTHOR]

In situ target biomolecule analysis is of great significance for real‐time monitoring and regulation of endogenous biomarkers and elementary biomolecules in vivo. Gratifyingly, the rapid evolution of structural DNA nanotechnology during past decades has established an appealing toolbox for biological analysis and medical detection. The modulated self‐assembly and underlying canonical Watson‐Crick base‐pairing rules provide possibilities for accurate controlling of the topologies and functions of obtained nanomaterials. The probes composed of diverse DNA nanostructures and DNA‐nanoparticle complexes can create a confined space, which increases target accessibility and improves probe stability, sensitivity and specificity. In this minireview, we retrospect the research progress of in‐situ biomolecular analysis based on DNA nanostructures for intracellular and in vivo biosensors in confined space. The characteristics of distinct DNA nanomaterials are first introduced, and then the fundamentals of biosensing process of designed DNA nanostructures are emphasized. Moreover, we elucidate our perspective over the challenges of this field and discuss the potential directions of this kind of application‐oriented fabrication technique. [ABSTRACT FROM AUTHOR]

In situ target biomolecule analysis is of great significance for real‐time monitoring and regulation of endogenous biomarkers and elementary biomolecules in vivo. Gratifyingly, the rapid evolution of structural DNA nanotechnology during past decades has established an appealing toolbox for biological analysis and medical detection. The modulated self‐assembly and underlying canonical Watson‐Crick base‐pairing rules provide possibilities for accurate controlling of the topologies and functions of obtained nanomaterials. The probes composed of diverse DNA nanostructures and DNA‐nanoparticle complexes can create a confined space, which increases target accessibility and improves probe stability, sensitivity and specificity. In this minireview, we retrospect the research progress of in‐situ biomolecular analysis based on DNA nanostructures for intracellular and in vivo biosensors in confined space. The characteristics of distinct DNA nanomaterials are first introduced, and then the fundamentals of biosensing process of designed DNA nanostructures are emphasized. Moreover, we elucidate our perspective over the challenges of this field and discuss the potential directions of this kind of application‐oriented fabrication technique. [ABSTRACT FROM AUTHOR]

In this study, we propose a microchip that is sequentially capable of fluorescently staining and washing DNAs. The main advantage of this microchip is that it allows for one-step preparation of small amounts of solution without degrading microscopic bio-objects such as the DNAs, cells, and biomolecules to be stained. The microchip consists of two inlets, the main channel, staining zone, washing zone, and one outlet, and was processed using a femtosecond laser system. High molecular transport of rhodamine B to deionized water was observed in the performance test of the microchip. Results revealed that the one-step procedure of on-chip DNA staining and washing was excellent compared to the conventional staining method. The one-step preparation of stained and washed DNAs through the microchip will be useful for preparing small volumes of experimental samples. [ABSTRACT FROM AUTHOR]

Reliable conformational sampling and trajectory analysis are always important to the study of the folding or binding mechanisms of biomolecules. Generally, one has to prepare many complicated parameters and follow a lot of steps to obtain the final data. The whole process is too complicated to new users. In this article, we provide a convenient and user‐friendly tool that is compatible to AMBER, called fast sampling and analysis tool (FSATOOL). FSATOOL has some useful features. First and the most important, the whole work is extremely simplified into two steps, one is the fast sampling procedure and the other is the trajectory analysis procedure. Second, it contains several powerful sampling methods for the simulation on graphics process unit, including our previous mixing replica exchange molecular dynamics method. The method combines the advantages of the biased and unbiased simulations. Finally, it extracts the dominant transition pathways automatically from the folding network by Markov state model. Users do not need to do the tedious intermediate steps by hand. To illustrate the usage of FSATOOL in practice, we perform one simulation for a RNA hairpin in explicit solvent. All the results are presented. © 2019 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The interaction of proteins with surfaces is a key phenomenon in many applications, but current understanding of the biophysics involved is lacking. At present, rational design of such emerging technologies is difficult as no methods or theories exist that correctly predict how surfaces influence protein behavior. Using molecular simulation and a coarse-grain model, this study illustrates for the first time that stability of proteins on surfaces can be correlated with tertiary structural elements for alpha-helical, orthogonal-bundle proteins. Results show that several factors contribute to stability on surfaces including the nature of the loop region where the tether is placed and the ability of the protein to freely rotate on the surface. A thermodynamic analysis demonstrates that surfaces stabilize proteins entropically and that any destabilization is an enthalpic effect. Moreover, the entropic effects are concentrated on the unfolded state of the protein while the ethalpic effects are focused on the folded state. [ABSTRACT FROM AUTHOR]

The description of the reorientational dynamics of flexible molecules is a challenging task, in particular when the rates of internal and global motions are comparable. The commonly used simple mode-decoupling models are based on the assumption of statistical independence between these motions. This assumption is not valid when the time scale separation between their rates is small, a situation that was found to arise in oligosaccharides in the context of certain internal motions. To make possible the interpretation of NMR spin relaxation data from such molecules, we developed a comprehensive approach generally applicable to flexible rotators with one internal degree of freedom. This approach integrates a stochastic description of coupled global tumbling and internal torsional motion, quantum chemical calculations of the local potential and the local geometry at the site of the restricted torsion, and hydrodynamics-based calculations of the diffusive properties. The method is applied to the disaccharide β-D-Glcp-(1→6)-α-D-[6-13C]-Manp-OMe dissolved in a DMSO-d6/D2O cryosolvent. The experimental NMR relaxation parameters, associated with the 13CH2 probe residing at the glycosidic linkage, include 13C T1 and T2 and 13C-{1H} nuclear Overhauser enhancement (NOE) as well as longitudinal and transverse dipole-dipole cross-correlated relaxation rates, acquired in the temperature range of 253–293 K. These data are predicted successfully by the new theory with only the H–C–H angle allowed to vary. Previous attempts to fit these data using mode-decoupling models failed. [ABSTRACT FROM AUTHOR]

In this paper, based on the integrated tempering sampling we introduce a selective integrated tempering sampling (SITS) method for the efficient conformation sampling and thermodynamics calculations for a subsystem in a large one, such as biomolecules solvated in aqueous solutions. By introducing a potential surface scaled with temperature, the sampling over the configuration space of interest (e.g., the solvated biomolecule) is selectively enhanced but the rest of the system (e.g., the solvent) stays largely unperturbed. The applications of this method to biomolecular systems allow highly efficient sampling over both energy and configuration spaces of interest. Comparing to the popular and powerful replica exchange molecular dynamics (REMD), the method presented in this paper is significantly more efficient in yielding relevant thermodynamics quantities (such as the potential of mean force for biomolecular conformational changes in aqueous solutions). It is more important that SITS but not REMD yielded results that are consistent with the traditional umbrella sampling free energy calculations when explicit solvent model is used since SITS avoids the sampling of the irrelevant phase space (such as the boiling water at high temperatures). [ABSTRACT FROM AUTHOR]

Mechanical unfolding of the fourth domain of Distyostelium discoideum filamin (DDFLN4) was studied by all-atom molecular dynamics simulations, using the GROMOS96 force field 43a1 and the simple point charge explicit water solvent. Our study reveals an important role of non-native interactions in the unfolding process. Namely, the existence of a peak centered at the end-to-end extension ΔR∼22 nm in the force-extension curve is associated with breaking of non-native hydrogen bonds. Such a peak has been observed in experiments but not in Go models, where non-native interactions are neglected. We predict that an additional peak occurs at ΔR∼2 nm using not only GROMOS96 force field 43a1 but also Amber 94 and OPLS force fields. This result would stimulate further experimental studies on elastic properties of DDFLN4. [ABSTRACT FROM AUTHOR]

Talaromyces marneffei and other Talaromyces species can cause opportunistic invasive fungal infections. We characterized clinical Talaromyces isolates from patients in California, USA, a non-Talaromyces-endemic area, by a multiphasic approach, including multigene phylogeny, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and phenotypic methods. We identified 10 potentially pathogenic Talaromyces isolates, 2 T. marneffei. [ABSTRACT FROM AUTHOR]

Circulating tumor cells (CTCs) are an important biomarker for various types of cancers. As CTCs are extremely rare in the bloodstream, the accurate analysis and efficient separation of CTCs is a challenging task. In order to develop new diagnostic approaches for cancer research, understanding the functional characteristics of biomolecules at the single-molecule level in individual cancer cells is required. Meanwhile, microfluidic platforms have emerged as a promising technology for analyzing single molecules and single cells. In this review, we discuss some label-free techniques for biomolecule detection and highlight some reports that have employed combined label-free techniques with microfluidics for individual molecule or cancer cell analysis. Finally, we offer our perspective of the integration of label-free techniques with microfluidic technology on future applications. • Label-free techniques were utilized for biomolecules detection. • Microfluidic were utilized for analyzing single molecules and single cells. • Analysis of biomolecule and CTCs based on label-free techniques with microfluidic. [ABSTRACT FROM AUTHOR]

Cells, as the fundamental structural elements and functional units of life, are necessary to be explored the variation of components and behaviors in the physiological and pathological processes. Benefited from the development of microfluidic culture and fluorescence labeling techniques, chips coupled with fluorescent tools have become a powerful platform for cell analysis. Thus, in this review, we mainly focus on the two aspects of overview: one is the microenvironment simulation on microfluidic systems including the fabrication of the chemical and physical microenvironment, the cell-cell co-culture/cell-extracellular matrix interaction model, and organ/tissue-on-a-chip system; the other is the fluorescence labeling strategies for cellular component detection and behavior observation, introducing from several aspects: nucleic acid-based modification, in situ chemical modification, hydrophobic insertion labeling and genetic-based labeling. At last, the existing achievements and future challenges in fluorescent analysis of cells based on microfluidic chip are discussed. • Analysis of cellular biomolecules and behavior plays a key role in understanding the pathological state of the cells. • This review summaries the various microenvironment simulation on microfluidic systems. • The fluorescence labeling strategies for imaging cellular biomolecules and behavior are introduced and discussed. [ABSTRACT FROM AUTHOR]

In this paper, we report on an integrated nanorod array as a novel sieving matrix for high-resolution separation of biomolecules. A wide size range of DNA (100 bp–166 kbp) and proteins (11.4 kDa–205 kDa) are resolved into sharp peaks within several minutes using devices with various pore apertures, either in a reptation mode or Ogston mechanism. The device delivers notable performance with the minimum resolvable size difference 10 bp for 100 bp and 150 bp DNA fragments, 15.9 kbp for 48 kbp and 166 kbp DNA chains, and 7.9 kDa for 11.4 and 68 kDa proteins, where the separation efficiency is higher than or comparable to other micro/nanofabricated artificial sieving structures. The process utilizes localized oblique angle deposition (LOAD) to simply integrate densely packed nanorods onto steep sidewalls of microfluidic channels, which eliminates the requirement of advanced lithography tools routinely used in conventional artificial sieving structures. We further demonstrate the modulation of pore aperture that employs the sculptured sidewalls by a custom deep reactive-ion etching (DRIE) recipe. Given the easy fabrication, excellent engineering control and outstanding sieving capability, this nanorod sieve device has great potentials to provide a simple and effective separation technique for biomolecule analysis. • A unique sieving matrix consisting of nanorod arrays was demonstrated for gel-free fractionation of DNA and proteins. • A wide size range of DNA (100 bp–166 kbp) and proteins (11.4 kDa–205 kDa) were resolved within several minutes. • A simple physical vapor deposition was utilized to easily integrate three dimensional oxide nanorods into separation device. [ABSTRACT FROM AUTHOR]

Introduction: Thiazolidinedione's are widely used synthetic antidiabetic agents. These agents affect the pumping power of heart muscle due to the formation of edema; limiting their usage in patients with congestive heart failure. The current study was aimed to perform in silico docking study of bioactive phytoconstituents from Cissus quadrangularis Linn. against the target Peroxisome proliferator-activated gamma (PPAR-γ). Materials and Methods: The docking study was performed by using AutoDock 4.2. The chemical constituents were retrieved from the PubChem database. The pharmacokinetic and toxicological parameters of each compound were predicted using PreADMET online server. The drug-likeness character of each compounds were predicted using Molsoft. Results: Quercetin scored highest drug-likeness character. Among the seven compounds, four compounds scored positive drug-likeness score. Qaudrangularin A showed highest binding affinity with the target protein. Discussion: All the compounds showed the binding affinity with the target protein suggesting that the compounds from Cissus quadrangularis can be utilized to target PPAR-γ in the management of diabetes. The study suggests supporting the current study by performing wet lab experiments. [ABSTRACT FROM AUTHOR]

Solution-state NMR typically requires 100 μM to 1 mM samples. This limitation prevents applications to mass-limited and aggregationprone target molecules. Photochemically induced dynamic nuclear polarization was adapted to data collection on low-concentration samples by radiofrequency gating, enabling rapid 1D NMR spectral acquisition on aromatic amino acids and proteins bearing aromatic residues at nanomolar concentration, i.e., a full order of magnitude below other hyperpolarization techniques in liquids. Both backbone H1-C13 and side-chain resonances were enhanced, enabling secondary and tertiary structure analysis of proteins with remarkable spectral editing, via the 13C PREPRINT pulse sequence. Laser-enhanced 2D NMR spectra of 5 μM proteins at 600 MHz display 30-fold better S/N than conventional 2D data collected at 900 MHz. Sensitivity enhancements achieved with this technology, denoted as low-concentration photo- CIDNP (LC-photo-CIDNP), depend only weakly on laser intensity, highlighting the opportunity of safer and more cost-effective hypersensitive NMR applications employing low-power laser sources. [ABSTRACT FROM AUTHOR]

In the 1970s, computer scientists began to engage in research in the field of structural biology. The first structural databases, as well as models and methods supporting the analysis of biomolecule structures, started to be created. RNA was put at the centre of scientific interest quite late. However, more and more methods dedicated to this molecule are currently being developed. This paper presents RNApolis - a new computing platform, which offers access to seven bioinformatic tools developed to support the RNA structure study. The set of tools include a structural database and systems for predicting, modelling, annotating and evaluating the RNA structure. RNApolis supports research at different structural levels and allows the discovery, establishment, and validation of relationships between the primary, secondary and tertiary structure of RNAs. The platform is freely available at http://rnapolis.pl [ABSTRACT FROM AUTHOR]

In recent times, fluorescent carbon quantum dots (CQDs) as an optical sensor have attained massive attention owing to their excellent optical properties. In current investigation, our group presented an easy and economical methodology to synthesize the nitrogen and phosphorous doped carbon quantum dots (N, P doped CQDs) for sensing dopamine (DA) and temperature in aqueous medium. The synthesized CQDs were characterized by using XRD, XPS, TEM, UV–Vis, FT-IR and fluorescence techniques. The N, P doped CQDs were synthesized via one-step microwave digestion method by using citric acid, ethylenediamine and urea phosphate as precursors. This method established the noble water solubility, good optical performances and fluorescence thermosensitivity of N, P doped CQDs. Also, N, P doped CQDs demonstrated a wide linear range of 10–500 μM (R2 = 0.994) and offered an electrifying detection limit of 0.021 μM for quantifying the dopamine. Moreover, this sensor possessed a good sensitivity, reversibility and linearity in the range of 10–70 °C. In addition, the CQDs sensing system repel the interference from probable foreign substances in real sample analysis, and attained good recoveries, which revealed the tremendous selectivity and adequate accuracy of the carbon quantum dots for sensing dopamine. The proposed N, P doped CQDs are simple as well as effective optical nanosensor and clasps venerable potential to widen the applications in analysis of biomolecules and other areas. Unlabelled Image • CQDs are highly water soluble, good dispersibility and stability. • Fluorescence quenching and detection mechanisms are explained well. • Synthesized CQDs are sensing the dopamine with good detection limits. • Real sample analysis has been done in human serum and urine samples. • CQDs displayed a good performance as a temperature sensor. [ABSTRACT FROM AUTHOR]

Abstract The development of atomic force microscopy (AFM) has opened up a wide range of novel opportunities in nanoscience and new modalities of observation in complex biological systems. AFM imaging has been widely employed to resolve the complex and heterogeneous conformational states involved in protein aggregation at the single molecule scale and shed light onto the molecular basis of a variety of human pathologies, including neurodegenerative disorders. The study of individual macromolecules at nanoscale, however, remains challenging, especially when fully quantitative information is required. In this review, we first discuss the principles of AFM with a special emphasis on the fundamental factors defining its sensitivity and accuracy. We then review the fundamental parameters and approaches to work at the limit of AFM resolution in order to perform single molecule statistical analysis of biomolecules and nanoscale protein aggregates. This single molecule statistical approach has proved to be powerful to unravel the molecular and hierarchical assembly of the misfolded species present transiently during protein aggregation, to visualise their dynamics at the nanoscale, as well to study the structural properties of amyloid-inspired functional nanomaterials. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Pecan nutshell could be used as carbon source for production of BC by G. entanii. • Cellulose produced by G. entanii had high purity. • BC production by G. entanii using pecan nutshell is the first report. • Data obtained can be useful for the synthesis of methylcellulose from other BC. Abstract Pecan nutshell is an abundant waste with a high content of carbohydrates. According to its chemical composition, pecan nutshell could be used as carbon source for Gluconacetobacter entanii , a bacterium that produces cellulose with high purity and nanometric characteristics. Bacterial cellulose (BC) was obtained from a static culture medium using pecan nutshell as carbon source and saccharose as control. Results showed that the pecan nutshell could be used as carbon source for production of BC. The cellulose yield ranged around 2.816 ± 0.040 g/L for 28 days. The morphological, structural and chemical properties of the cellulose produced were similar to those reported for others BC. The spectroscopic characterization indicated the chemical functionalization of BC and the reduction of its crystallinity. The production of BC with G. entanii using pecan nutshell as carbon source, is the first report. The BC could have potential use in chemical functionalization and in the preparation of biocomposites. [ABSTRACT FROM AUTHOR]

Abstract This paper demonstrates the use of a smartphone-based sensor for fluorescence polarization (FP) analysis of biomolecules. The FP detection can rapidly sense ligand-analyte bindings by measuring molecule mobility, and thus, FP-based assays have been widely used for rapid diagnostics in clinics. Here, we implemented the FP detection apparatus using a 3D-printed compact holder and the built-in camera of a smartphone. The system offers accurate measurements of the degree of polarization by simultaneously detecting the fluorescence intensities parallel and perpendicular to the polarization of the excitation. The fluorescence signal of the sample is excited by a laser or light-emitting diode and separated by a polarization beam cube depending on the polarization. Parallel and perpendicular polarized emissions are projected onto two different regions of the sensor chip in the smartphone camera. A custom software app was developed to count the average intensity in the areas of interest and compute the degree of polarization. We validated the system by measuring the polarization of dye molecules dissolved in solutions with different viscosities. As an example of biomolecule sensing, a competitive FP immunoassay of Prostaglandin E 2 was demonstrated using the developed system and exhibited the limit of detection of 1.57 ng/mL. The smartphone-based FP assay platform can also be implemented for the detection of toxins, disease biomarkers, and pathogens in resource-limited settings. Highlights • A smartphone-based detector is designed for fluorescence polarization immunoassays. • A rapid and wash-free assay is developed for biomolecule analysis using smartphone. • The smartphone detector can quantify dinoprostone in 30 minutes. • The system has the potential for disease diagnosis in resource-limited settings. [ABSTRACT FROM AUTHOR]

Abstract Surface plasmon resonance (SPR) biosensors have become an important label-free optical biomolecular sensing technology and a "gold standard" for retrieving information on the kinetics of biomolecular interactions. Even though biomolecules typically contain an abundance of easily ionizable chemical groups, there is a gap in understanding of whether (and how) the electrostatic charge of a biomolecular system influences the SPR biosensor response. In this work we show that negative static charge present in a biomolecular layer on the surface of an SPR sensor results in significant SPR spectral shifts, and we identify two major mechanisms responsible for such shifts: 1) the formation of an electrical double layer (ionic mechanism), and 2) changes in the electron density at the surface of a metal (electronic mechanism). We show that under low ionic strength conditions, the electronic mechanism is dominant and the SPR wavelength shift is linearly proportional to the surface concentration of biomolecular charges. At high ionic strength conditions, both electric and ionic mechanisms contribute to the SPR wavelength shift. Using the electronic mechanism, we estimated the pKa of surface-bound carboxylic groups and the relative concentration of the carboxyl-terminated alkanethiols in a binary self-assembled monolayer of alkanethiols. The reported sensitivity of SPR to surface charge is especially important in the context of biomolecular sensing. Moreover, it provides an avenue for the application of SPR sensors for fast, label-free determination of the net charge of a biomolecular coating, which is of interest in material science, surface chemistry, electrochemistry, and other fields. Highlights • Electrostatic charge on immobilized or detected biomolecules influences the SPR biosensor response. • We identify 2 mechanisms: 1) formation of an electrical double layer and 2) change in electron density at the metal surface. • Charge-induced SPR shifts should be considered in interpretation of SPR data. • The effect allows new applications of SPR biosensors, e.g. surface charge quantification, acidobasic equilibria studies, etc. [ABSTRACT FROM AUTHOR]

Abstract Advances in nanostructured materials have facilitated the development of novel sensitive techniques for detection of environmental and clinical analytes. There is immense need for development of devices that can detect analytes at concentrations as low as few pg mL−1. The comparable size of nanostructured materials and biomolecules enabled the integration of biological systems with nanometer sized structures. Herein, we demonstrate a Zinc Oxide nanorods (ZnONRs) integrated ultrasensitive label-free biosensor with femtomolar (0.01 pg mL−1) sensitivity for the endocrine disruptor 17 β -Estradiol (E2). The ZnONRs, average width 50 nm and length 325 nm, were grown on the silver electrode surface (Ag-ZnONRs). Monoclonal antibodies of E2 (mAb-E2) were covalently immobilized on ZnONRs surface and measured using electrochemical impedance spectroscopy (EIS). A linear detection range of 0.1–200 pg mL−1 for E2 with R2 = 0.99 and % RSD = 4.35 (n = 3, assay volume 90 µL) was achieved for the developed nano-sensing system. A significant enhancement in the sensitivity was achieved in the presence of ZnONRs, enabling the limit of quantification down to 0.1 pg mL−1 with 2.7 % capacitance change per decade. In addition, a further increase in sensitivity due to assay volume reduction (20 µL) was observed enabling further scope of miniaturization. Highlights ● ZnO nanorods based ultrasensitive nanoimmunosensor for 17 β -Estradiol. ● Significant enhancement in sensitivity (2×) achieved using ZnONR. ● An astounding limit of detection, 0.01 pg mL−1 for E2 was achieved. [ABSTRACT FROM AUTHOR]

Engineered nanomaterials hold promise for a wide range of applications in medicine. However, safe use of nanomaterials requires that interactions with biological systems, not least with the immune system, are understood. Do nanomaterials elicit novel or unexpected effects, or is it possible to predict immune responses to nanomaterials based on how the immune system handles pathogens? How does the bio-corona of adsorbed biomolecules influence subsequent immune interactions of nanomaterials? How does the grafting of polymers such as poly(ethylene glycol) onto nanomaterial surfaces impact on these interactions? Can ancient immune evasion or "stealth" strategies of pathogens inform the design of nanomaterials for biomedical applications? Can nanoparticles co-opt immune cells to target diseased tissues? The answers to these questions may prove useful for the development of nanomedicines. [ABSTRACT FROM AUTHOR]

Axial coordination is a crucial biological process to regulate biomolecules' functions in natural enzymes. However, it is a great challenge to determine the single or dual axial interaction between the metal center of enzymes and the ligand. In this work, a controllable axial coordination system was developed based on G‐quadruplex/hemin complex by designing a series of fluorescent derivatives. The mechanism on axial coordination of G‐quadruplex/hemin with coumarin‐imidazole ligands was proposed to be single‐sided, and led to fluorescence quenching of ligands. Upon addition of nitric oxide, the fluorescence of ligands was recovered through competitive axial coordination, providing a "signal on" strategy for signal transduction. More significantly, the fluorescent imaging of intracellular nitric oxide was achieved after conjugating with gold nanoparticles. Also, the proposed protocol provided a smart strategy to monitor the relationship between nitric oxide and p53 protein activity in living cells. Single‐sided axial coordination of G‐quadruplex‐hemin complex shows significant advantages of highly reactive monomeric hemin, a single available axial site, and a strong binding capacity compared with uncomplexed hemin, which can be used as a molecular switch for in situ imaging and detection of intracellular NO through competitive axial coordination after assembly with a designed fluorescent ligand and conjugated with the nanocarrier. [ABSTRACT FROM AUTHOR]

Extracellular vesicles (EVs) actively participate in intercellular communication and pathological processes. Studying the molecular signatures of EVs is key to reveal their biological functions and clinical values, which, however, is greatly hindered by their sub‐100 nm dimensions, the low quantities of biomolecules each EV carries, and the large population heterogeneity. Now, single‐EV flow cytometry analysis is introduced to realize single EV counting and phenotyping in a conventional flow cytometer for the first time, enabled by target‐initiated engineering (TIE) of DNA nanostructures on each EV. By illuminating multiple markers on single EVs, statistically significant differences are revealed among the molecular signatures of EVs originating from several breast cancer cell lines, and the cancer cell‐derived EVs among the heterogeneous EV populations are successfully recognized. Thus, our approach holds great potential for various biological and biomedical applications. Single extracellular vesicle (EV) flow cytometry analysis enabled by target‐initiated engineering (TIE) of DNA nanostructures reveals unique molecular signatures of individual vesicles and differentiates EV sub‐populations. [ABSTRACT FROM AUTHOR]

Abstract Cryogenic electron microscopy (cryo-EM) and single-particle analysis enables determination of near-atomic resolution structures of biological molecules. However, large computational requirements limit throughput and rapid testing of new image processing tools. We developed PRIME, an algorithm part of the SIMPLE software suite, for determination of the relative 3D orientations of single-particle projection images. PRIME has primarily found use for generation of an initial ab initio 3D reconstruction. Here we show that the strategy behind PRIME, iterative estimation of per-particle orientation distributions with stochastic hill climbing, provides a competitive approach to near-atomic resolution single-particle 3D reconstruction. A number of mathematical techniques for accelerating the convergence rate are introduced, leading to a speedup of nearly two orders of magnitude. We benchmarked our developments on numerous publicly available data sets and conclude that near-atomic resolution ab initio 3D reconstructions can be obtained with SIMPLE in a matter of hours, using standard over-the-counter CPU workstations. [ABSTRACT FROM AUTHOR]

Recent advances in cellular analysis revealed that the seemingly identical cells are heterogeneous in term of functionality, compositions, and genetic performance. These differences cause difficulty in the diagnostic for a specific model of disease. Detection of biomolecules such as DNA, RNA, and protein or analysis of cell(s), detection of cell surface molecules, and secreted protein, can help us to improve the understanding of a targeted disease and development of new diagnostic and therapeutic approaches. A single‐cell includes the minute quantity of these target molecules. Microfluidic devices have the ability to capture a single‐cell and its lysate into a pico or femtoliter volumes droplet, or micro‐well thus preventing dilution and limiting diffusion. In this review we described the advancement and limitations in microfluidic techniques used toward single‐cells analysis. In systematic life sciences, in order to obtain mammalian tissue and then crushing it to a single‐cell for analysis using microfluidic platform five major levels can be categorized. The isolated single‐cells are prone to on‐chip or off‐chip analysis for the targeted biomolecules. [ABSTRACT FROM AUTHOR]

PEGylated superparamagnetic Fe 3 O 4 nanoparticles were prepared using co-precipitation method and analyzed by using X-ray diffraction (XRD), UV–Visible spectroscopy, Fourier-transform infrared (FTIR), Transmission electron microscopy (TEM), Dynamic light scattering (DLS), Vibrating sample magnetometer (VSM) and TG analysis. The XRD results showed that an FCC phase of the Fe 3 O 4 structure was formed by an average lattice constant about 8.379 Å. From optical absorbance spectra, the linear absorption coefficient and the band gap of PEGylated Fe 3 O 4 nanoparticles were measured 0.855 cm −1 and 2.27 eV, respectively. The magnetic characteristics indicated that the PEGylated Fe 3 O 4 nanoparticles had the saturation magnetic moments of 61 emug −1 . The measurements of nonlinear optical (NLO) properties of PEGylated Fe 3 O 4 nanoparticles have been performed using a nanosecond Nd:YAG pulse laser at 532 nm by the Z-scan technique. Both bare and PEGylated Fe 3 O 4 nanoparticles clearly were exhibited a negative NLO index of refraction at 532 nm. A nonlocality in NLO response of nanoparticles was observed after PEGylation. The NLO absorption of PEGylated Fe 3 O 4 nanoparticles is attributed to 2-photon absorption. A good NLO absorption was observed for both bare and PEG-coated Fe 3 O 4 nanoparticles at 532 nm. Moreover, the nonlinear susceptibility of PEG-coated Fe 3 O 4 nanoparticles was determined by the Z-scan technique of the order of 10 −9 esu. The outcomes suggest that PEGylated Fe 3 O 4 nanoparticles may be a promising candidate for the NLO applications. [ABSTRACT FROM AUTHOR]

Abstract It has been two decades since the lipid raft hypothesis was first presented. Even today, whether these nanoscale cholesterol-rich domains are present in cell membranes is not completely resolved. However, especially in the last few years, a rich body of literature has demonstrated both the presence and the importance of non-random distribution of biomolecules on the membrane, which is the focus of this review. These new developments have pushed the experimental limits of detection and have brought us closer to observing lipid domains in the plasma membrane of live cells. Characterization of biomolecules associated with lipid rafts has revealed a deep connection between biological regulation and function and membrane compositional heterogeneities. Finally, tantalizing new developments in the field have demonstrated that lipid domains might not just be associated with the plasma membrane of eukaryotes but could potentially be a ubiquitous membrane-organizing principle in several other biological systems. This article is part of a Special Issue entitled: Emergence of Complex Behavior in Biomembranes edited by Marjorie Longo. Graphical abstract Unlabelled Image Highlights • Emergence of evidence showing compositional heterogeneity in plasma membrane • Functional organization of lipids is important for signaling and pathogen entry. • Lipid mediated organization is an emergent theme in diverse biological systems. [ABSTRACT FROM AUTHOR]

Abstract: Reporter strains have proven to be powerful tools to study Mycobacterium tuberculosis (Mtb) physiology. Transcriptional and translational reporter strains are engineered by fusing a readout gene, encoding a fluorescent, luminescent or enzymatic protein, downstream of a promoter or in‐frame with a gene of interest. When the reporter is expressed, it generates a signal that acts as a synthetic phenotype, enabling the study of physiologies that might have otherwise been hidden. This review will discuss approaches for generating reporter strains in Mtb and how they can be used as tools for high‐throughput genetic and small molecule screening and as biomarkers for examining Mtb responses to drug or immune stresses during animal infections. Fluorescent reporter strains have an added benefit in that they can be used for single‐cell studies both in vitro and in vivo, thus enabling the study of mechanisms underlying phenotypic heterogeneity. Recent examples of the use of Mtb reporter strains will be presented with a focus on how they can be used as tools for drug discovery and development. © 2018 IUBMB Life, 70(9):818–825, 2018 [ABSTRACT FROM AUTHOR]

Graphical abstract Abstract Colloidal silver (Ag) nanoparticles (AgNP) have been widely used for surface-enhanced Raman spectroscopy (SERS) applications. We report a simple, rapid and effective method to prepare AgNP colloids for SERS using the classic organic chemistry Ag mirror reaction with Tollens’ reagent. The AgNP colloid prepared with this process was characterized using SEM, and the reaction conditions further optimized using SERS measurements. It was found that Ag mirror reaction conditions that included 20 mM AgNO 3 , 5 min reaction time, and 0.5 M glucose produced AgNP colloids with an average size of 319.1 nm (s.d ± 128.1). These AgNP colloids exhibited a significant SERS response when adenine was used as the reporter molecule. The usefulness of these new AgNP colloids was demonstrated by detecting the nucleotides adenosine 5′-mono-phosphate (AMP), guanosine 5′-monophosphate (GMP), cytidine 5′-monophosphate (CMP), and uridine 5′-monophosphate (UMP). A detection limit of 500 nM for AMP was achieved with the as-prepared AgNP colloid. The bacterium Mycoplasma pneumoniae was also easily detected in laboratory culture with these SERS substrates. These findings attest to the applicability of this AgNP colloid for the sensitive and specific detection of both small biomolecules and microorganisms. [ABSTRACT FROM AUTHOR]

Carbon monoxide (CO) has long been known as the “silent killer” owing to its ability to form carboxyhemoglobin—the main cause of CO poisoning in humans. Its role as an endogenous neurotransmitter, however, was suggested in the early 1990s. Since then, the biological activity of CO has been widely examined via both the direct administration of CO and in the form of so-called “carbon monoxide releasing molecules (CORMs).” This overview will explore the general physiological effects and potential therapeutic applications of CO when delivered in the form of CORMs. [ABSTRACT FROM AUTHOR]

Despite the increasingly popular application of the quartz crystal microbalance (QCM) technique in monitoring phenomena taking place at solid–liquid interfaces, ranging from changes in mass to changes in conformation, a simple, direct relationship between QCM signal and surface mass remains elusive. In this paper, we report that the proportional relationship between the QCM signal and the surface mass arises from the linear relationship between the viscosity of the layer adsorbed at the solid–liquid interface and the surface coverage, as well as a small viscosity shift. The proportionality coefficient depends on the intrinsic viscosity of adsorbates, solvent density, and quartz crystal thickness. The intrinsic viscosity is dominated by the conformation of the entire molecular chain and the adsorption blob for end-grafted and physisorbed molecules, respectively. Using this modified Sauerbrey equation, the phenomena relating to the conformation of discrete chains at the solid–liquid interfaces can be semi-quantitatively described. [ABSTRACT FROM AUTHOR]

DNA-based switches are structure-switching biomolecules widely employed in different bioanalytical applications. Of particular interest are DNA–based switches whose activity is regulated through the use of allostery. Allostery is a naturally occurring mechanism in which ligand binding induces the modulation and fine control of a connected biomolecule function as a consequence of changes in concentration of the effector. Through this general mechanism, many different allosteric DNA-based switches able to respond in a highly controlled way at the presence of a specific molecular effector have been engineered. Here, we discuss how to design allosterically regulated DNA-based switches and their applications in the field of molecular sensing, diagnostic and drug release. [ABSTRACT FROM AUTHOR]

Ion mobility (IM) is rapidly gaining attention for the separation and analysis of biomolecules due to the ability to distinguish the shapes of ions. However, conventional constant electric field drift tube IM separations have limited resolving power, constrained by practical limitations on the path length and maximum applied voltage. The implementation of traveling waves (TW) in IM removes the latter limitation, allowing higher resolution to be achieved using extended path lengths. Both of these can be readily obtained in structures for lossless ion manipulations (SLIM), which are fabricated from arrays of electrodes patterned on two parallel surfaces where potentials are applied to generate appropriate electric fields between the surfaces. Here we have investigated the relationship between the primary SLIM variables, such as electrode dimensions, inter-surface gap, and the applied TW voltages, that directly impact the fields experienced by ions. Ion trajectory simulations and theoretical calculations have been utilized to understand the dependence of SLIM geometry and effective electric fields on IM resolution. The variables explored impact both ion confinement and the observed IM resolution using SLIM modules. [ABSTRACT FROM AUTHOR]

Simultaneous detection and differentiation of biomolecules is of significance in biological research. Biothiols such as cysteine (Cys), homocysteine (Hcy), and glutathione (GSH) play an important role in regulating the vital functions of living organisms. However, existing methods for simultaneous detection and differentiation of Cys, Hcy, and GSH are still challenging because of their similarity in structure and chemical properties. Herein we report a probe that simultaneously detects and discriminates between mixtures of Cys, Hcy and GSH using 19 F nuclear magnetic resonance (NMR). This 19 F NMR probe responds rapidly to biothiols through the Michael addition reaction and subsequent intramolecular cyclization reaction allowing differentiation between Cys, Hcy and GSH through 19 F NMR chemical shift. We demonstrate that this 19 F NMR probe is a powerful method for analysis of complex mixtures. [ABSTRACT FROM AUTHOR]

Measurement of small molecules in extremely dilute concentrations of analyte play an important role in different issues ranging from food industry to biological, pharmaceutical and therapeutical applications. Surface plasmon resonance (SPR) sensors can be a suitable choice for detection of small molecules based on interactions with biomolecules. However, sensitivity of the system for detection of these molecules is very low. Improving sensitivity has been a challenge for years. Therefore, different methods have been used to enhance SPR signals. The SPR signal enhancement using numerous nanomaterials has provided exciting results. Among various nanomaterials, metal nanoparticles (for instance gold, silver and magnetic nanoparticles), quantum dots, nanorads, and carbon-based nanostructures have got much attention due to ease in fabrication, appropriate size and shape. In addition to the advantages provided by using nanomaterials, signal enhancement provided by the appropriate use of phase information of the reflected light could be also important to improve SPR sensitivity. Phase-sensitive SPR sensors are able to detect infinitesimal changes in external properties of target while traditional type of SPR cannot demonstrate these changes. This article provides an overview on signal enhancment in SPR using nanomaterials and properties of light. We also discuss on recent progresses of the field, describing basic concepts concerning nanostructures as well as phase-sensitive sensors as platform for enhancement of signal in SPR. [ABSTRACT FROM AUTHOR]

A microfluidic paper-based analytical device (μPAD) was simply constructed for highly sensitive detection of L -glutamic acid and L -cysteine. The μPAD featured with two functional zones on one strip of paper achieved by preferable multi-plate ZnO nanoflowers (ZnO NFs) and molecularly imprinting polymer (MIP) membranes. The as-designed μPAD was established based on the inherent relation between the photo-oxidation products and photoelectrochemical (PEC) performance with the highly sensitive detection of biomolecules. The ZnO NFs were utilized to produce photo-oxidation products by driving the reaction between ferrocenemethanol and photogenerated holes under ultraviolet light. The photo-oxidation products easily flowed to MIP membranes along the hydrophilic channel via capillary action. MIP membranes as the receptors specifically recognized the analytes as well as decreased the electron loss by blocking the reduction reaction between electrons and photo-oxidation products. The PEC response was obtained in the processes of electrons transfer and exhibited the direct relationships corresponding to the concentrations of target analytes. The μPAD showed the detection limits toward L -glutamic acid and L -cysteine as low as 9.6 pM and 24 pM, respectively. Moreover, it is interesting to point out that ZnO NFs nanostructure shows superior PEC signal compared with those of ZnO nanospheres, nanosheets, and nanorod arrays. In current work, photo-oxidation products are utilized to achieve highly sensitive PEC detection for biomolecules under ultraviolet light as well as avoid the effects of multiple modifications in the same region on the reproducibility, which is beneficial for opening up rich possibility for designing more efficient analytical strategy. [ABSTRACT FROM AUTHOR]

Electrochemical (bio)sensors have attracted much attention due to their high sensitivity, fast response time, biocompatibility, low cost and easy miniaturization. Specially, ever-growing necessity and interest have given rise to the fast development of electrochemical (bio)sensors for the detection of small biomolecules. They play enormous roles in the life processes with various biological function, such as life signal transmission, genetic expression and metabolism. Moreover, their amount in body can be used as an indicator for diagnosis of many diseases. For example, an abnormal concentration of blood glucose can indicate hyperglycemia or hypoglycemia. Graphene (GR) shows great applications in electrochemical (bio)sensors. Compared with two-dimensional (2D) GR that is inclined to stack together due to the strong π-π interaction, monolithic 3D porous GR has larger specific area, superior mechanical strength, better stability, higher conductivity and electrocatalytic activity. So they attracted more and increasing attention as sensing materials for small biomolecules. This review focuses on the recent advances and strategies in the fabrication methods of 3D porous GR and the development of various electrochemical (bio)sensors based on porous GR and its nanocomposites for the detection of small biomolecules. The challenges and future efforts direction of high-performance electrochemical (bio)sensors based on 3D porous GR for more sensitive analysis of small biomolecules are discussed and proposed. It will give readers an overall understanding of their progress and provide some theoretical guidelines for their future efforts and development. [ABSTRACT FROM AUTHOR]

Parametric separation of carbon nanotubes, especially based on their length is a challenge for a number of nano-tech researchers. We demonstrate a method to combine bio-conjugation, SDS-PAGE, and silver staining in order to separate carbon nanotubes on the basis of length. Egg-white lysozyme, conjugated covalently onto the single-walled carbon nanotubes surfaces using carbodiimide method. The proposed conjugation of a biomolecule onto the carbon nanotubes surfaces is a novel idea and a significant step forward for creating an indicator for length-based carbon nanotubes separation. The conjugation step was followed by SDS-PAGE and the nanotube fragments were precisely visualized using silver staining. This high precision, inexpensive, rapid and simple separation method obviates the need for centrifugation, additional chemical analyses, and expensive spectroscopic techniques such as Raman spectroscopy to visualize carbon nanotube bands. In this method, we measured the length of nanotubes using different image analysis techniques which is based on a simplified hydrodynamic model. The method has high precision and resolution and is effective in separating the nanotubes by length which would be a valuable quality control tool for the manufacture of carbon nanotubes of specific lengths in bulk quantities. To this end, we were also able to measure the carbon nanotubes of different length, produced from different sonication time intervals. [ABSTRACT FROM AUTHOR]

Abstract: Emerging applications in the field of chemical biology are currently limited by the lack of bioorthogonal reactions allowing both removal and linkage of chemical entities on complex biomolecules. We recently discovered a novel reaction between iminosydnones and strained alkynes leading to two products resulting from ligation and fragmentation of iminosydnones under physiological conditions. We now report the synthesis of a panel of substituted iminosydnones and the structure reactivity relationship between these compounds and strained alkyne partners. This study identified the most relevant substituents, which allow to increase the rate of the transformation and to develop a bifunctional cleavable linker with improved kinetics. [ABSTRACT FROM AUTHOR]

Investigations of static or dynamic interactions between proteins or other biological macromolecules in living cells often rely on the use of fluorescent tags with two different colors in conjunction with adequate theoretical descriptions of Förster Resonance Energy Transfer (FRET) and molecular-level micro-spectroscopic technology. One such method based on these general principles is FRET spectrometry, which allows determination of the quaternary structure of biomolecules from cell-level images of the distributions, or spectra of occurrence frequency of FRET efficiencies. Subsequent refinements allowed combining FRET frequency spectra with molecular concentration information, thereby providing the proportion of molecular complexes with various quaternary structures as well as their binding/dissociation energies. In this paper, we build on the mathematical principles underlying FRET spectrometry to propose two new spectrometric methods, which have distinct advantages compared to other methods. One of these methods relies on statistical analysis of color mixing in subpopulations of fluorescently tagged molecules to probe molecular association stoichiometry, while the other exploits the color shift induced by FRET to also derive geometric information in addition to stoichiometry. The appeal of the first method stems from its sheer simplicity, while the strength of the second consists in its ability to provide structural information. [ABSTRACT FROM AUTHOR]

Abstract: Weak ligand–receptor recognition events are often amplified by recruiting multiple regulatory biomolecules to the action site in biological systems. However, signal amplification in in vitro biomimetic systems generally lack the spatiotemporal regulation in vivo. Herein we report a framework nucleic acid (FNA)‐programmed strategy to develop valence‐controlled signal amplifiers with high modularity for ultrasensitive biosensing. We demonstrated that the FNA‐programmed signal amplifiers could recruit nucleic acids, proteins, and inorganic nanoparticles in a stoichiometric manner. The valence‐controlled signal amplifier enhanced the quantification ability of electrochemical biosensors, and enabled ultrasensitive detection of tumor‐relevant circulating free DNA (cfDNA) with sensitivity enhancement of 3–5 orders of magnitude and improved dynamic range. [ABSTRACT FROM AUTHOR]

Chemical imaging provides new insight into the fundamental atomic, molecular, and biochemical composition of tissue and how they are interrelated in normal physiology. Visualising and quantifying products of pathogenic reactions long before structural changes become apparent also adds a new dimension to understanding disease pathogenesis. While chemical imaging in isolation is somewhat limited by the nature of information it can provide (e.g. peptides, metals, lipids, or functional groups), integrating immunohistochemistry allows simultaneous, targeted imaging of biomolecules while also mapping tissue composition. Together, this approach can provide invaluable information on the inner workings of the cell and the molecular basis of diseases. [ABSTRACT FROM AUTHOR]