The conformational dynamics of individual, flexible polymers in steady shear flow were directly observed by the use of video fluorescence microscopy. The probability distribution for the molecular extension was determined as a function of shear rate, ␥, for two different polymer relaxation times, . In contrast to the behavior in pure elongational flow, the average polymer extension in shear flow does not display a sharp coil-stretch transition. Large, aperiodic temporal fluctuations were observed, consistent with end-over-end tumbling of the molecule. The rate of these fluctuations (relative to the relaxation rate) increased as the Weissenberg number, ␥, was increased.The dynamics of flexible polymers in shear is of great practical interest because this type of flow occurs whenever a fluid flows past a surface. Macroscopic, non-Newtonian rheological properties of polymer solutions, such as flow-dependent viscosities and normal stresses, result from microscopic stresses that arise when polymeric molecules are stretched and affect the solvent motion. Thus, much effort has been directed at predicting the molecular dynamics of polymers in shear flows (1-5). However, it has been difficult to rigorously test these predictions because the dynamics of a polymer molecule in shear have not been observed directly. Experimental efforts have mainly focused on measuring bulk rheological properties or on measuring the scattering of light or neutrons by polymer solutions (6 -10). Here we describe how single-molecule imaging techniques (11) can be used to study the configurations of polymers in shear flow so that the detailed molecular predictions of theories can be tested.It has long been recognized that the amount of distortion of a molecule is strongly dependent on the nature of the flow (4, 5). In general, any planar flow of the form v ជ ϭ v x x ϩ v y ŷ may be represented as a linear superposition of a rotational flow with a vorticity ϭ [(‫ץ‬v y / ‫ץ‬x) Ϫ (‫ץ‬v x /‫ץ‬y)]/2 and an elongational flow with a strain rate ϭ [(‫ץ‬v y /‫ץ‬x) ϩ (‫ץ‬v x /‫ץ‬y)]/2. In a pure elongational flow ( ϭ 0) one expects large deformations of a polymer, whereas in a pure rotational flow ( ϭ 0) one expects only rotation and not deformation (4,5).Most practical flows consist of a mixture of both rotational and elongational components, and the resulting polymer deformation depends on the relative magnitudes of and . In general, the response is not necessarily a linear superposition of the responses to each component. In a simple shear flow (v y ϭ 0 and v x ϭ ␥y, where ␥ ϭ dv x /dy is the shear rate) the magnitude of the elongational and rotational components are equal ( ϭ ) (Fig. 1A). In this case, it has been suggested that the polymer will not attain a stable, strongly stretched state (4, 5). In fact, large fluctuations in the extension due to an end-over-end tumbling of the molecule have been observed in some simulations (3). These fluctuations presumably occur because the stretched state is destabilized by the rotational component of the sh...

Anyone who has used a light microscope has wished that its resolution could be a little better. Now, after centuries of gradual improvements, fluorescence microscopy has made a quantum leap in its resolving power due, in large part, to advancements over the past several years in a new area of research called super-resolution fluorescence microscopy. In this Primer, we explain the principles of various super-resolution approaches, such as STED, (S)SIM, and STORM/(F)PALM. Then, we describe recent applications of super-resolution microscopy in cells, which demonstrate how these approaches are beginning to provide new insights into cell biology, microbiology, and neurobiology.

Influenza is a paradigm for understanding viral infections. As an opportunistic pathogen exploiting the cellular endocytic machinery for infection, influenza is also a valuable model system for exploring the cell's constitutive endocytic pathway. We have studied the transport, acidification, and fusion of single influenza viruses in living cells by using real-time fluorescence microscopy and have dissected individual stages of the viral entry pathway. The movement of individual viruses revealed a striking three-stage active transport process that preceded viral fusion with endosomes starting with an actin-dependent movement in the cell periphery, followed by a rapid, dynein-directed translocation to the perinuclear region, and finally an intermittent movement involving both plus-and minus-end-directed microtubule-based motilities in the perinuclear region. Surprisingly, the majority of viruses experience their initial acidification in the perinuclear region immediately following the dynein-directed rapid translocation step. This finding suggests a previously undescribed scenario of the endocytic pathway toward late endosomes: endosome maturation, including initial acidification, largely occurs in the perinuclear region.T he infection pathway of influenza is a complex, multistep process: viruses enter cells by receptor-mediated endocytosis, then move from endocytic vesicles to early endosomes and finally to late endosomes where the viruses fuse with the endosomal membrane to release viral genes (1-7), a pathway followed by many other medically important viruses (3, 4). Exploiting the cell's constitutive endocytic machinery for infection, influenza is an ideal probe for exploring the cell's endocytic pathway. However, despite intensive efforts in investigating influenza infection, many critical properties of the endocytosis and endocytic traffic of the virus remain elusive. Among these are important and general questions for cellular endocytosis: what are the transport mechanisms of endocytic compartments at different stages on the endocytic pathway, and how do these compartments and the enclosed endocytic cargo mature (6-8)?The difficulty in real-time imaging of the endocytic pathway presents one of the major hurdles in addressing the above questions. In this work, by tracking the behavior of single influenza viruses in real-time (9-12), we have dissected individual stages of the viral entry process, observed transient, previously unobserved steps in endocytic viral trafficking, and obtained a dynamic picture of the cell's endocytic pathway exploited by influenza. We have discovered that virus-bearing endosomes are transported in cells in three distinct stages, each with a distinct cytoskeleton-and motor-protein-dependent mechanism. We have revealed surprising endocytic acidification dynamics: the initial acidification of endocytic cargo mainly occurs in the perinuclear region, bringing into question the previous picture that early endosomes in the cell periphery are the early acidification sites for endocytic ca...

Using fluorescence microscopy, we studied the catalysis by and folding of individual Tetrahymena thermophila ribozyme molecules. The dye-labeled and surface-immobilized ribozymes used were shown to be functionally indistinguishable from the unmodified free ribozyme in solution. A reversible local folding step in which a duplex docks and undocks from the ribozyme core was observed directly in single-molecule time trajectories, allowing the determination of the rate constants and characterization of the transition state. A rarely populated docked state, not measurable by ensemble methods, was observed. In the overall folding process, intermediate folding states and multiple folding pathways were observed. In addition to observing previously established folding pathways, a pathway with an observed folding rate constant of 1 per second was discovered. These results establish single-molecule fluorescence as a powerful tool for examining RNA folding.

We have studied the correlation between structural dynamics and function of the hairpin ribozyme. The enzyme-substrate complex exists in either docked (active) or undocked (inactive) conformations. Using single-molecule fluorescence methods, we found complex structural dynamics with four docked states of distinct stabilities and a strong memory effect where each molecule rarely switches between different docked states. We also found substrate cleavage to be rate-limited by a combination of conformational transitions and reversible chemistry equilibrium. The complex structural dynamics quantitatively explain the heterogeneous cleavage kinetics common to many catalytic RNAs. The intimate coupling of structural dynamics and function is likely a general phenomenon for RNA.

Actin, spectrin, and associated molecules form a periodic sub-membrane lattice structure in axons. How this membrane skeleton is developed and why it preferentially forms in axons are unknown. Here, we studied the developmental mechanism of this lattice structure. We found that this structure emerged early during axon development and propagated from proximal regions to distal ends of axons. Components of the axon initial segment were recruited to the lattice late during development. Formation of the lattice was regulated by the local concentration of βII spectrin, which is higher in axons than in dendrites. Increasing the dendritic concentration of βII spectrin by overexpression or by knocking out ankyrin B induced the formation of the periodic structure in dendrites, demonstrating that the spectrin concentration is a key determinant in the preferential development of this structure in axons and that ankyrin B is critical for the polarized distribution of βII spectrin in neurites.DOI: http://dx.doi.org/10.7554/eLife.04581.001

Image-based approaches to single-cell transcriptomics, in which RNA species are identified and counted in situ via imaging, have emerged as a powerful complement to single-cell methods based on RNA sequencing of dissociated cells. These image-based approaches naturally preserve the native spatial context of RNAs within a cell and the organization of cells within tissue, which are important for addressing many biological questions. However, the throughput of these imagebased approaches is relatively low. Here we report advances that lead to a drastic increase in the measurement throughput of multiplexed error-robust fluorescence in situ hybridization (MERFISH), an imagebased approach to single-cell transcriptomics. In MERFISH, RNAs are identified via a combinatorial labeling approach that encodes RNA species with error-robust barcodes followed by sequential rounds of single-molecule fluorescence in situ hybridization (smFISH) to read out these barcodes. Here we increase the throughput of MERFISH by two orders of magnitude through a combination of improvements, including using chemical cleavage instead of photobleaching to remove fluorescent signals between consecutive rounds of smFISH imaging, increasing the imaging field of view, and using multicolor imaging. With these improvements, we performed RNA profiling in more than 100,000 human cells, with as many as 40,000 cells measured in a single 18-h measurement. This throughput should substantially extend the range of biological questions that can be addressed by MERFISH.single-cell analysis | fluorescence | in situ hybridization | transcriptomics | multiplexed imaging

Imaging membranes in live cells with nanometer-scale resolution promises to reveal ultrastructural dynamics of organelles that are essential for cellular functions. In this work, we identified photoswitchable membrane probes and obtained super-resolution fluorescence images of cellular membranes. We demonstrated the photoswitching capabilities of eight commonly used membrane probes, each specific to the plasma membrane, mitochondria, the endoplasmic recticulum (ER) or lysosomes. These small-molecule probes readily label live cells with high probe densities. Using these probes, we achieved dynamic imaging of specific membrane structures in living cells with 30-60 nm spatial resolution at temporal resolutions down to 1-2 s. Moreover, by using spectrally distinguishable probes, we obtained two-color super-resolution images of mitochondria and the ER. We observed previously obscured details of morphological dynamics of mitochondrial fusion/fission and ER remodeling, as well as heterogeneous membrane diffusivity on neuronal processes.nanoscopy | diffraction limit | photoswitchable dye | stochastic optical reconstruction microscopy | photoactivation localization microscopy