Single-molecule imaging of cell surfaces using near-field nanoscopy

Living cells use surface molecules such as receptors and sensors to acquire information about and to respond to their environments. The cell surface machinery regulates many essential cellular processes, including cell adhesion, tissue development, cellular communication, inflammation, tumor metastasis, and microbial infection. These events often involve multimolecular interactions occurring on a nanometer scale and at very high molecular concentrations. Therefore, understanding how single-molecules localize, assemble, and interact on the surface of living cells is an important challenge and a difficult one to address because of the lack of high-resolution single-molecule imaging techniques. In this Account, we show that atomic force microscopy (AFM) and near-field scanning optical microscopy (NSOM) provide unprecedented possibilities for mapping the distribution of single molecules on the surfaces of cells with nanometer spatial resolution, thereby shedding new light on their highly sophisticated functions. For single-molecule recognition imaging by AFM, researchers label the tip with specific antibodies or ligands and detect molecular recognition signals on the cell surface using either adhesion force or dynamic recognition force mapping. In single-molecule NSOM, the tip is replaced by an optical fiber with a nanoscale aperture. As a result, topographic and optical images are simultaneously generated, revealing the spatial distribution of fluorescently labeled molecules. Recently, researchers have made remarkable progress in the application of near-field nanoscopy to image the distribution of cell surface molecules. Those results have led to key breakthroughs: deciphering the nanoscale architecture of bacterial cell walls; understanding how cells assemble surface receptors into nanodomains and modulate their functional state; and understanding how different components of the cell membrane (lipids, proteins) assemble and communicate to confer efficient functional responses upon cell activation. We anticipate that the next steps in the evolution of single-molecule near-field nanoscopy will involve combining single-molecule imaging with single-molecule force spectroscopy to simultaneously measure the localization, elasticity, and interactions of cell surface molecules. In addition, progress in high-speed AFM should allow researchers to image single cell surface molecules at unprecedented temporal resolution. In parallel, exciting advances in the fields of photonic antennas and plasmonics may soon find applications in cell biology, enabling true nanoimaging and nanospectroscopy of individual molecules in living cells.     

Association of Synthetic Polymers

Abstract

The methods available for a quantitative evaluation of solutions of associating macro-molecules are reviewed. Association is defined as a rapid equilibrium between unimers (non-associated molecules) and multimers (associated molecules) in homogeneous solutions. It can be subdivided into open and closed associations. Open associations are consecutive processes. Closed associations represent all-or-none processes. Both types of associations can be of either the end-to-end type (number of associogenic sites independent of molecular weight) or the segment-to-segment type (number of associogenic sites increasing with molecular weight in a polymerhomologue series). Relations between the polymolecularity of the unimers and the polydispersity of the multimers are given. Viscometry is shown to be no reliable method for the investigation of association if used alone without the knowledge of thermodynamic data. The equilibrium constants of macromolecules seem to be higher than those of low molecular weight materials of similar constitution under comparable conditions. The association of polypropylenes increases with increasing syndiotacticity. A possible influence of the order of the solvent and of the desolvation processes on the equilibrium constants of association is discussed. Poly(γ-benzyl-L-glutamates) form cyclic multimers in dilute solutions of certain solvents and solvent mixtures.     

Irreversibility,Energy Dissipation,and Time Effects in Intermolecular and Surface Interactions

The use of thermodynamic functions such as surface energy (y) or the reversible work of adhesion (W) implicitly assumes that two surfaces are interacting under conditions of thermodynamic equilibrium. Likewise, the concept of the adhesion force or pressure between two surfaces, molecules, or colloidal particles also suggests the existence of well-defined time-independent values for these quantities. Yet most interactions involving molecules, surfaces, and complex fluid systems are irreversible, involving the transfer of energy from one system to another; that is, they involve “energy dissipation”. We review the molecular origins nonequilibrium (irreversible) interactions of surfaces that give rise to adhesion hysteresis, contact angle hysteresis, friction, and other thin-film properties, and discuss the important role of “time” in such processes which can have a significant effect on what we measure. We also consider the possible central role of nonequilibrium interactions in biological systems, where nature often makes use of the finite time of molecular processes for regulating the interactions of proteins, membranes, and cells.     

Nanoscale ear drum: graphene based nanoscale sensors

The difficulty in determining the mass of a sample increases as its size diminishes. At the nanoscale, there are no direct methods for resolving the mass of single molecules or nanoparticles and so more sophisticated approaches based on electromechanical phenomena are required. More importantly, one demands that such nanoelectromechanical techniques could provide not only information about the mass of the target molecules but also about their geometrical properties. In this sense, we report a theoretical study that illustrates in detail how graphene membranes can operate as nanoelectromechanical mass-sensor devices. Wide graphene sheets were exposed to different types and amounts of molecules and molecular dynamic simulations were employed to treat these doping processes statistically. We demonstrate that the mass variation effect and information about the graphene-molecule interactions can be inferred through dynamical response functions. Our results confirm the potential use of graphene as a mass detector device with remarkable precision in estimating variations in mass at the molecular scale and other physical properties of the dopants.     

Infrared optical activity: electric field approaches in time domain

Vibrational circular dichroism (VCD) spectroscopy provides detailed information about the absolute configurations of chiral molecules including biomolecules and synthetic drugs. This method is the infrared (IR) analogue of the more popular electronic CD spectroscopy that uses the ultraviolet and visible ranges of the electromagnetic spectrum. Because conventional electronic CD spectroscopy measures the difference in signal intensity, problems such as weak signal and low time-resolution can limit its utility. To overcome the difficulties associated with that approach, we have recently developed femtosecond IR optical activity (IOA) spectrometry, which directly measures the IOA free-induction-decay (FID), the impulsive chiroptical IR response that occurs over time. In this Account, we review the time-domain electric field measurement and calculation methods used to simultaneously characterize VCD and related vibrational optical rotatory dispersion (VORD) spectra. Although conventional methods measure the electric field intensity, this vibrational technique is based on a direct phase-and-amplitude measurement of the electric field of the chiroptical signal over time. This method uses a cross-polarization analyzer to carry out heterodyned spectral interferometry. The cross-polarization scheme enables us to selectively remove the achiral background signal, which is the dominant noise component present in differential intensity measurement techniques. Because we can detect the IOA FID signal in a phase-amplitude-sensitive manner, we can directly characterize the time-dependent electric dipole/magnetic dipole response function and the complex chiral susceptibility that contain information about the angular oscillations of charged particles. These parameters yield information about the VCD and VORD spectra. In parallel with such experimental developments, we have also calculated the IOA FID signal and the resulting VCD spectrum. These simulations use a quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) method and calculate the electric dipole/magnetic dipole cross-correlation function in the time domain. Although many quantum chemistry calculation approaches can only consider a limited number of geometry-optimized conformations of chiral molecules in a gas phase, this computational method includes the solute-solvent interactions and the inhomogeneous distributions of solute conformers in condensed phases. A subsequent Fourier transformation of the chiral response function produced a theoretical VCD spectrum in the entire mid-IR frequency range. Directly comparing theory and experiment, we demonstrate quantitative agreement between frequency-tunable femtosecond IOA measurements and QM/MM MD simulations of (1S)-β-pinene in CCl(4) solution. We anticipate that these direct IOA measurement and calculation methods will be applied to the studies of equilibrium chiroptical properties and structure determinations. These methods provide tools to investigate ultrafast structural dynamics of chiral systems with unprecedented time resolution.     

Scanning probe microscopy of atoms and molecules on insulating films: from imaging to molecular manipulation

Scanning tunneling microscopy (STM) and atomic force microscopy (AFM) of single atoms and molecules on ultrathin insulating films have led to a wealth of novel observations and insights. Based on the reduced electronic coupling to the metallic substrate, these techniques allow the charge state of individual atoms to be controlled, orbitals of individual molecules to be imaged and metal-molecule complexes to be built up. Near-contact AFM adds the unique capabilities of imaging and probing the chemical structure of single molecules with atomic resolution. With the help of atomic/molecular manipulation techniques, chemical binding processes and molecular switches can be studied in detail.     

Differential Polarization Imaging of Plant Cells. Mapping the Anisotropy of Cell Walls and Chloroplasts

Modern light microscopy imaging techniques have substantially advanced our knowledge about the ultrastructure of plant cells and their organelles. Laser-scanning microscopy and digital light microscopy imaging techniques, in general—in addition to their high sensitivity, fast data acquisition, and great versatility of 2D–4D image analyses—also opened the technical possibilities to combine microscopy imaging with spectroscopic measurements. In this review, we focus our attention on differential polarization (DP) imaging techniques and on their applications on plant cell walls and chloroplasts, and show how these techniques provided unique and quantitative information on the anisotropic molecular organization of plant cell constituents: (i) We briefly describe how laser-scanning microscopes (LSMs) and the enhanced-resolution Re-scan Confocal Microscope (RCM of Confocal.nl Ltd. Amsterdam, Netherlands) can be equipped with DP attachments—making them capable of measuring different polarization spectroscopy parameters, parallel with the ‘conventional’ intensity imaging. (ii) We show examples of different faces of the strong anisotropic molecular organization of chloroplast thylakoid membranes. (iii) We illustrate the use of DP imaging of cell walls from a variety of wood samples and demonstrate the use of quantitative analysis. (iv) Finally, we outline the perspectives of further technical developments of micro-spectropolarimetry imaging and its use in plant cell studies.     

Chemical engineering of cellular processes

Processes conducted by living cells determine the quantity and quality of our food, medicines, environment and our personal health and vitality. The functions of cells in these contexts are determined primarily by networks of specific catalytic and noncovalent interactions. The nature and activities of these networks are dictated by the DNA in the cell and the history of the cell's environment, thereby defining the ways in which engineers can influence cellular function. The onslaught of quantitative and qualitative knowledge in molecular biology, combined with the emergence of powerful and precise genetic, biochemical, chemical, analytical, and mathematical technologies, have defined the working framework and the needed tools for a systematic chemical engineering approach to creation and optimization of cellular processes to serve better the needs of mankind and our environment. Several recent examples demonstrate how chemical engineers are mobilizing this information and capability to address critical problems in bioprocessing, medicine, and in the generation of new molecules and materials. These examples illustrate the ability of chemical engineers to be more actively involved in the creation of products and processes, an essential endeavor for the future vitality of the profession.     

Structural and Functional Insights into the Transmembrane Domain Association of Eph Receptors

Eph receptors are the largest family of receptor tyrosine kinases and by interactions with ephrin ligands mediate a myriad of processes from embryonic development to adult tissue homeostasis. The interaction of Eph receptors, especially at their transmembrane (TM) domains is key to understanding their mechanism of signal transduction across cellular membranes. We review the structural and functional aspects of EphA1/A2 association and the techniques used to investigate their TM domains: NMR, molecular modelling/dynamics simulations and fluorescence. We also introduce transmembrane peptides, which can be used to alter Eph receptor signaling and we provide a perspective for future studies.     

Observation of molecular inhibition and binding structures of amyloid peptides

Unveiling interactions between labeling molecules and amyloid fibrils is essential to develop new detection methods for studying amyloid structures under various conditions. This review endeavours to reflect the progress in studying interactions between molecular inhibitors and amyloid peptides using a series of experimental approaches, such as X-ray diffraction, nuclear magnetic resonance, scanning probe microscopy, and electron microscopy. The revealed binding mechanisms of anti-amyloid drugs and target proteins could benefit the rational design of drugs for prevention or treatment of amyloidal diseases.     

Unravel the Local Complexity of Biological Environments by MALDI Mass Spectrometry Imaging

Classic metabolomic methods have proven to be very useful to study functional biology and variation in the chemical composition of different tissues. However, they do not provide any information in terms of spatial localization within fine structures. Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) does and reaches at best a spatial resolution of 0.25 μm depending on the laser setup, making it a very powerful tool to analyze the local complexity of biological samples at the cellular level. Here, we intend to give an overview of the diversity of the molecules and localizations analyzed using this method as well as to update on the latest adaptations made to circumvent the complexity of samples. MALDI MSI has been widely used in medical sciences and is now developing in research areas as diverse as entomology, microbiology, plant biology, and plant–microbe interactions, the rhizobia symbiosis being the most exhaustively described so far. Those are the fields of interest on which we will focus to demonstrate MALDI MSI strengths in characterizing the spatial distributions of metabolites, lipids, and peptides in relation to biological questions.     

Melatonin Regulates Aging and Neurodegeneration through Energy Metabolism,Epigenetics, Autophagy and Circadian Rhythm Pathways

Brain aging is linked to certain types of neurodegenerative diseases and identifying new therapeutic targets has become critical. Melatonin, a pineal hormone, associates with molecules and signaling pathways that sense and influence energy metabolism, autophagy, and circadian rhythms, including insulin-like growth factor 1 (IGF-1), Forkhead box O (FoxOs), sirtuins and mammalian target of rapamycin (mTOR) signaling pathways. This review summarizes the current understanding of how melatonin, together with molecular, cellular and systemic energy metabolisms, regulates epigenetic processes in the neurons. This information will lead to a greater understanding of molecular epigenetic aging of the brain and anti-aging mechanisms to increase lifespan under healthy conditions.     

Luminescence studies of polymer behaviour

Luminescence techniques can be used to study polymer systems both as an analytical tool and as a means of studying molecular behaviour. In the latter context, some very interesting information may be obtained on a variety of molecular and energy transport processes. Measurements of luminescence intensity and quenching can be used to observe electronic energy transfer processes (both along polymer chains and from polymer chains to additive molecules). These have a technical importance in that they are the photophysical processes which precede the chemical phenomena important in photodegradation or photostabilisation of polymers. The basic criteria for energy transfer are introduced and examples are given of “down-chain” energy migration coefficients for a number of polymers. Studies of the depolarisation of luminescence can be used as a measurement of rotation in the electronic excited state of the photoactive group. Fluorescence depolarisation is introduced and examples are given of processes with nanosecond relaxation times. The concept of phosphorescence depolarisation is also mentioned, and the first use of this to study processes with millisecond relaxation times is illustrated.     

客体分子数对甲烷水合物导热性能影响的分子动力学模拟

本文通过采用EMD方法Green-Kubo理论计算263.15 K 晶穴占有率0-100% sI甲烷水合物导热系数,研究客体分子数对甲烷水合物导热性能的影响。模拟结果显示,甲烷水合物的低导热性能由主体分子构建的笼型结构决定。而在相同温压条件下,随着客体分子甲烷进入晶胞数目增多,晶穴占有率增大后,密度增大,同时客体分子对声子的散射也增强,二者均导致导热性能增强。     

Single Molecule Fluorescence Detection and Tracking in Mammalian Cells: The State-of-the-Art and Future Perspectives

Insights from single-molecule tracking in mammalian cells have the potential to greatly contribute to our understanding of the dynamic behavior of many protein families and networks which are key therapeutic targets of the pharmaceutical industry. This is particularly so at the plasma membrane, where the method has begun to elucidate the mechanisms governing the molecular interactions that underpin many fundamental processes within the cell, including signal transduction, receptor recognition, cell-cell adhesion, etc. However, despite much progress, single-molecule tracking faces challenges in mammalian samples that hinder its general application in the biomedical sciences. Much work has recently focused on improving the methods for fluorescent tagging of target molecules, detection and localization of tagged molecules, which appear as diffraction-limited spots in charge-coupled device (CCD) images, and objectively establishing the correspondence between moving particles in a sequence of image frames to follow their diffusive behavior. In this review we outline the state-of-the-art in the field and discuss the advantages and limitations of the methods available in the context of specific applications, aiming at helping researchers unfamiliar with single molecules methods to plan out their experiments.     

π-Conjugated cyanostilbene derivatives: a unique self-assembly motif for molecular nanostructures with enhanced emission and transport

π-Conjugated organic molecules represent an attractive platform for the design and fabrication of a wide range of nano- and microstructures for use in organic optoelectronics. The desirable optical and electrical properties of π-conjugated molecules for these applications depend on their primary molecular structure and their intermolecular interactions such as molecular packing or ordering in the condensed states. Because of the difficulty in satisfying these rigorous structural requirements for photoluminescence and charge transport, the development of novel high-performance π-conjugated systems for nano-optoelectronics has remained a challenge. This Account describes our recent discovery of a novel class of self-assembling π-conjugated organic molecules with a built-in molecular elastic twist. These molecules consist of a cyano-substituted stilbenic π-conjugated backbone and various terminal functional groups, and they offer excellent optical, electrical, and self-assembly properties for use in various nano-optoelectronic devices. The characteristic "twist elasticity" behavior of these molecules occurs in response to molecular interactions. These large torsional or conformational changes in the cyanostilbene backbone play an important role in achieving favorable intermolecular interactions that lead to both high photoluminescence and good charge carrier mobility in self-assembled nanostructures. Conventional π-conjugated molecules in the solid state typically show concentration (aggregation) fluorescence quenching. Initially, we describe the unique photoluminescence properties, aggregation-induced enhanced emission (AIEE), of these new cyanostilbene derivatives that elegantly circumvent these problems. These elastic twist π-conjugated backbones serve as versatile scaffolds for the preparation of well-defined patterned nanosized architectures through facile self-assembly processes. We discuss in particular detail the preparation of 1D nanowire structures through programmed self-assembly. This Account describes the importance of utilizing AIEE effects to explore optical device applications, such as organic semiconducting lasers (OSLs), optical memory, and sensors. We demonstrate the rich electronic properties, including the electrical conductivity, field-effect carrier mobility, and electroluminescence of highly crystalline 1D nanowire and coaxial donor-acceptor nanocable structures composed of elastic twist π-conjugated molecules. The electronic properties were measured using various techniques, including current-voltage (I-V), conducting-probe atomic force microscopy (CP-AFM), and space-charge-limited-current (SCLC) measurements. We prepared and characterized several electronic device structures, including organic field-effect transistors (OFETs) and organic light-emitting field-effect transistors (OLETs).     

Intercellular Communication in the Central Nervous System as Deduced by Chemical Neuroanatomy and Quantitative Analysis of Images: Impact on Neuropharmacology

In the last decades, new evidence on brain structure and function has been acquired by morphological investigations based on synergic interactions between biochemical anatomy approaches, new techniques in microscopy and brain imaging, and quantitative analysis of the obtained images. This effort produced an expanded view on brain architecture, illustrating the central nervous system as a huge network of cells and regions in which intercellular communication processes, involving not only neurons but also other cell populations, virtually determine all aspects of the integrative function performed by the system. The main features of these processes are described. They include the two basic modes of intercellular communication identified (i.e., wiring and volume transmission) and mechanisms modulating the intercellular signaling, such as cotransmission and allosteric receptor–receptor interactions. These features may also open new possibilities for the development of novel pharmacological approaches to address central nervous system diseases. This aspect, with a potential major impact on molecular medicine, will be also briefly discussed.     

Host-Guest Complexation Studied by Fluorescence Correlation Spectroscopy: Adamantane�CCyclodextrin Inclusion

The host-guest complexation between an Alexa 488 labelled adamantane derivative and β-cyclodextrin is studied by Fluorescence Correlation Spectroscopy (FCS). A 1:1 complex stoichiometry and a high association equilibrium constant of K = 5.2 × 10⁴ M⁻¹ are obtained in aqueous solution at 25 °C and pH = 6. The necessary experimental conditions are discussed. FCS proves to be an excellent method for the determination of stoichiometry and association equilibrium constant of this type of complexes, where both host and guest are nonfluorescent and which are therefore not easily amenable to standard fluorescence spectroscopic methods.     

Contrast Agents for Photoacoustic and Thermoacoustic Imaging: A Review

Photoacoustic imaging (PAI) and thermoacoustic imaging (TAI) are two emerging biomedical imaging techniques that both utilize ultrasonic signals as an information carrier. Unique advantages of PAI and TAI are their abilities to provide high resolution functional information such as hemoglobin and blood oxygenation and tissue dielectric properties relevant to physiology and pathology. These two methods, however, may have a limited detection depth and lack of endogenous contrast. An exogenous contrast agent is often needed to effectively resolve these problems. Such agents are able to greatly enhance the imaging contrast and potentially break through the imaging depth limit. Furthermore, a receptor-targeted contrast agent could trace the molecular and cellular biological processes in tissues. Thus, photoacoustic and thermoacoustic molecular imaging can be outstanding tools for early diagnosis, precise lesion localization, and molecular typing of various diseases. The agents also could be used for therapy in conjugation with drugs or in photothermal therapy, where it functions as an enhancer for the integration of diagnosis and therapy. In this article, we present a detailed review about various exogenous contrast agents for photoacoustic and thermoacoustic molecular imaging. In addition, challenges and future directions of photoacoustic and thermoacoustic molecular imaging in the field of translational medicine are also discussed.