Living Cells as Test Tubes

Future of biomedical sciences: single molecule microscopy

The behavior of single molecule defines whether a cell lives, dies, or responds to a specific drug treatment. Single molecule microscopies have begun to reveal the number, location, and functionalities of molecules outside and inside living cells. This issue of Biopolymers presents a first set of reviews that aim to highlight the accomplishments and future prospects of single molecule microscopies.

Multiple association states between glycine receptors and gephyrin identified by SPT analysis

The scaffolding protein gephyrin is known to anchor glycine receptors (GlyR) at synapses and to participate in the dynamic equilibrium between synaptic and extrasynaptic GlyR in the neuronal membrane. Here we investigated the properties of this interaction in cells cotransfected with YFP-tagged gephyrin and GlyR subunits possessing an extracellular myc-tag. In HeLa cells and young neurons, single particle tracking was used to follow in real time individual GlyR, labeled with quantum dots, traveling into and out of gephyrin clusters. Analysis of the diffusion properties of two GlyR subunit types--able or unable to bind gephyrin--gave access to the association states of GlyR with its scaffolding protein. Our results indicated that an important portion of GlyR could be linked to a few molecules of gephyrin outside gephyrin clusters. This emphasizes the role of scaffolding proteins in the extrasynaptic membrane and supports the implication of gephyrin-gephyrin interactions in the stabilization of GlyR at synapses. The kinetic parameters controlling the equilibrium between GlyR inside and outside clusters were also characterized. Within clusters, we identified two subpopulations of GlyR with distinct degrees of stabilization between receptors and scaffolding proteins.

Under the microscope: single molecule symposium at the University of Michigan, 2006

In recent years, a revolution has occurred in the basic sciences, which exploits novel single molecule detection and manipulation tools to track and analyze biopolymers in unprecedented detail. A recent Gordon Research Conference style meeting, hosted by the University of Michigan, highlighted current status and future perspectives of this rising field as researchers begin to integrate it with mainstream biology and nanotechnology.

A versatile multimode microscope to probe and manipulate nanoparticles and biomolecules

We describe a flexible, multifaceted optical setup that allows quantitative measurement and manipulation of biomolecules and nanoparticles in biomimetic and cellular systems. We have implemented integrated biophotonics techniques (i.e. differential interference contrast, wide-field fluorescence, prism- and objective-based total internal reflection excitation, single particle tracking, fluorescence correlation spectroscopy and dynamic holographic optical trapping) on a single platform. The adaptability of this versatile, custom-designed system allows us to simultaneously monitor cell morphology, while measuring lateral diffusion of biomolecules or controlling their cellular location or interaction partners.

A survey of single-molecule techniques in chemical biology

Single-molecule methods have revolutionized scientific research by rendering the investigation of once-inaccessible biological processes amenable to scientific inquiry. Several of the more established techniques will be emphasized in this Review, including single-molecule fluorescence microscopy, optical tweezers, and atomic force microscopy, which have been applied to many diverse biological processes. Serving as a taste of all the exciting research currently underway, recent examples will be discussed of translocation of RNA polymerase, myosin VI walking, protein folding, and enzyme activity. We will end by providing an assessment of what the future holds, including techniques that are currently in development.

UltraSOFAST HMQC NMR and the Repetitive Acquisition of 2D Protein Spectra at Hz Rates

Following unidirectional biophysical events such as the folding of proteins or the equilibration of binding interactions, requires experimental methods that yield information at both atomic-level resolution and at high repetition rates. Toward this end a number of different approaches enabling the rapid acquisition of 2D NMR spectra have been recently introduced, including spatially encoded "ultrafast" 2D NMR spectroscopy and SOFAST HMQC NMR. Whereas the former accelerates acquisitions by reducing the number of scans that are necessary for completing arbitrary 2D NMR experiments, the latter operates by reducing the delay between consecutive scans while preserving sensitivity. Given the complementarities between these two approaches it seems natural to combine them into a single tool, enabling the acquisition of full 2D protein NMR spectra at high repetition rates. We demonstrate here this capability with the introduction of "ultraSOFAST" HMQC NMR, a spatially encoded and relaxation-optimized approach that can provide 2D protein correlation spectra at approximately 1 s repetition rates for samples in the approximately 2 mM concentration range. The principles, relative advantages, and current limitations of this new approach are discussed, and its application is exemplified with a study of the fast hydrogen-deuterium exchange characterizing amide sites in Ubiquitin.

Chemical crosshairs on the central dogma

As cellular machines and processes that regulate the flow of genomic information have come into sharper focus, a new level of chemical control has become possible. The scope of such chemical intervention extends from the mechanistic dissection of biochemical processes in living cells to the targeted control of gene networks and cell fate.

Monitoring dynamic systems with multiparameter fluorescence imaging

A new general strategy based on the use of multiparameter fluorescence detection (MFD) to register and quantitatively analyse fluorescence images is introduced. Multiparameter fluorescence imaging (MFDi) uses pulsed excitation, time-correlated single-photon counting and a special pixel clock to simultaneously monitor the changes in the eight-dimensional fluorescence information (fundamental anisotropy, fluorescence lifetime, fluorescence intensity, time, excitation spectrum, fluorescence spectrum, fluorescence quantum yield, distance between fluorophores) in real time. The three spatial coordinates are also stored. The most statistically efficient techniques known from single-molecule spectroscopy are used to estimate fluorescence parameters of interest for all pixels, not just for the regions of interest. Their statistical significance is judged from a stack of two-dimensional histograms. In this way, specific pixels can be selected for subsequent pixel-based subensemble analysis in order to improve the statistical accuracy of the parameters estimated. MFDi avoids the need for sequential measurements, because the registered data allow one to perform many analysis techniques, such as fluorescence-intensity distribution analysis (FIDA) and fluorescence correlation spectroscopy (FCS), in an off-line mode. The limitations of FCS for counting molecules and monitoring dynamics are discussed. To demonstrate the ability of our technique, we analysed two systems: (i) interactions of the fluorescent dye Rhodamine 110 inside and outside of a glutathione sepharose bead, and (ii) microtubule dynamics in live yeast cells of Schizosaccharomyces pombe using a fusion protein of Green Fluorescent Protein (GFP) with Minichromosome Altered Loss Protein 3 (Mal3), which is involved in the dynamic cycle of polymerising and depolymerising microtubules.

From imaging to understanding: Frontiers in Live Cell Imaging, Bethesda, MD, April 19-21, 2006

A recent meeting entitled Frontiers in Live Cell Imaging was attended by more than 400 cell biologists, physicists, chemists, mathematicians, and engineers. Unlike typical special topics meetings, which bring together investigators in a defined field primarily to review recent progress, the purpose of this meeting was to promote cross-disciplinary interactions by introducing emerging methods on the one hand and important biological applications on the other. The goal was to turn live cell imaging from a "technique" used in cell biology into a new exploratory science that combines a number of research fields.