Microscale visualization of cellular features in adult macaque visual cortex.

Expansion microscopy and light sheet imaging enable fine-scale resolution of intracellular features that comprise neural circuits. Most current techniques visualize sparsely distributed features across whole brains or densely distributed features within individual brain regions. Here, we visualize dense distributions of immunolabeled proteins across early visual cortical areas in adult macaque monkeys. This process may be combined with multiphoton or magnetic resonance imaging to produce multimodal atlases in large, gyrencephalic brains.

Connecting single-cell transcriptomes to projectomes in mouse visual cortex.

The mammalian brain is composed of diverse neuron types that play different functional roles. Recent single-cell RNA sequencing approaches have led to a whole brain taxonomy of transcriptomically-defined cell types, yet cell type definitions that include multiple cellular properties can offer additional insights into a neuron's role in brain circuits. While the Patch-seq method can investigate how transcriptomic properties relate to the local morphological and electrophysiological properties of cell types, linking transcriptomic identities to long-range projections is a major unresolved challenge. To address this, we collected coordinated Patch-seq and whole brain morphology data sets of excitatory neurons in mouse visual cortex. From the Patch-seq data, we defined 16 integrated morpho-electric-transcriptomic (MET)-types; in parallel, we reconstructed the complete morphologies of 300 neurons. We unified the two data sets with a multi-step classifier, to integrate cell type assignments and interrogate cross-modality relationships. We find that transcriptomic variations within and across MET-types correspond with morphological and electrophysiological phenotypes. In addition, this variation, along with the anatomical location of the cell, can be used to predict the projection targets of individual neurons. We also shed new light on infragranular cell types and circuits, including cell-type-specific, interhemispheric projections. With this approach, we establish a comprehensive, integrated taxonomy of excitatory neuron types in mouse visual cortex and create a system for integrated, high-dimensional cell type classification that can be extended to the whole brain and potentially across species.

Single-cell transcriptomic evidence for dense intracortical neuropeptide networks.

Seeking new insights into the homeostasis, modulation and plasticity of cortical synaptic networks, we have analyzed results from a single-cell RNA-seq study of 22,439 mouse neocortical neurons. Our analysis exposes transcriptomic evidence for dozens of molecularly distinct neuropeptidergic modulatory networks that directly interconnect all cortical neurons. This evidence begins with a discovery that transcripts of one or more neuropeptide precursor (NPP) and one or more neuropeptide-selective G-protein-coupled receptor (NP-GPCR) genes are highly abundant in all, or very nearly all, cortical neurons. Individual neurons express diverse subsets of NP signaling genes from palettes encoding 18 NPPs and 29 NP-GPCRs. These 47 genes comprise 37 cognate NPP/NP-GPCR pairs, implying the likelihood of local neuropeptide signaling. Here, we use neuron-type-specific patterns of NP gene expression to offer specific, testable predictions regarding 37 peptidergic neuromodulatory networks that may play prominent roles in cortical homeostasis and plasticity.

Carbon Nanotubes: Solution for the Therapeutic Delivery of siRNA?

Carbon nanotubes have many unique physical and chemical properties that are being widely explored for potential applications in biomedicine especially as transporters of drugs, proteins, DNA and RNA into cells. Specifically, single-walled carbon nanotubes (SWCNT) have been shown to deliver siRNA to tumors in vivo. The low toxicity, the excellent membrane penetration ability, the protection afforded against blood breakdown of the siRNA payload and the good biological activity seen in vivo suggests that SWCNT may become universal transfection vehicles for siRNA and other RNAs for therapeutic applications. This paper will introduce a short review of a number of therapeutic applications for carbon nanotubes and provide recent data suggesting SWCNT are an excellent option for the delivery of siRNA clinically.

Compartmentalization of the outer hair cell demonstrated by slow diffusion in the extracisternal space.

In the outer hair cell (OHC), the extracisternal space (ECiS) is a conduit and reservoir of the molecular and ionic substrates of the lateral wall, including those necessary for electromotility. To determine the mechanisms through which molecules are transported in the ECiS of the OHC, we selectively imaged the time-dependent spatial distribution of fluorescent molecules in a <100 nm layer near the cell/glass interface of the recording chamber after their photolytic activation in a diffraction-limited volume. The effective diffusion coefficient was calculated using the analytical solution of the diffusion equation. It was found that diffusion in the ECiS is isotropic and not affected by depolarizing the OHC. Compared with free solution, the diffusion of 10 kDa dextran was slowed down in both the ECiS and the axial core by a factor of 4.6 and 1.6, respectively.

Fast two-dimensional standing-wave total-internal-reflection fluorescence microscopy using acousto-optic deflectors.

We report a scheme for 2D standing-wave total-internal-reflection fluorescence microscopy. Standing-wave patterns are generated by two interfering beams coupled through the objective lens. Period, angular orientation, and phase of standing waves are controlled entirely by acousto-optic deflectors. The lateral resolution improvement of 100 nm is combined with an axial selectivity of <100 nm by utilizing an evanescent standing-wave pattern. This technique can provide real-time imaging of subresolution structures in live biological specimens near a glass-water interface.

Metastable liquid clusters in super- and undersaturated protein solutions.

Dense liquid phases, metastable with respect to a solid phase, but stable with respect to the solution, have been known to form in solutions of proteins and small-molecule substances. Here, with the protein lumazine synthase as a test system, using dynamic and static light scattering and atomic force microscopy, we demonstrate submicron size clusters of dense liquid. In contrast to the macroscopic dense liquid, these clusters are metastable not only with respect to the crystals, but also with respect to the low-concentration solution: the characteristic cluster lifetime is limited to approximately 10 s, after which they decay. The cluster population is detectable only if they occupy >10(-6) of the solution volume and have a number density >105 cm-3 for 3 to 11% of the monitored time. The cluster volume fraction varies within wide limits and reaches up to 10(-3). Increasing protein concentration increases the frequency of cluster detection but does not affect the ranges of the cluster sizes, suggesting that a preferred cluster size exists. A simple Monte Carlo model with protein-like potentials reproduces the metastable clusters of dense liquid with limited lifetimes and variable sizes and suggests that the mean cluster size is determined by the kinetics of growth and decay and not by thermodynamics.

Standing wave total internal reflection fluorescence microscopy to measure the size of nanostructures in living cells.

We present the first application of standing wave fluorescence microscopy (SWFM) to determine the size of biological nanostructures in living cells. The improved lateral resolution of less than 100 nm enables superior quantification of the size of subcellular structures. We demonstrate the ability of SWFM by measuring the diameter of biological nanotubes (membrane tethers formed between cells). The combination of SWFM with total internal reflection (TIR), referred to as SW-TIRFM, allows additional improvement of axial resolution by selective excitation of fluorescence in a layer of about 100 nm.

A metastable prerequisite for the growth of lumazine synthase crystals.

Dense liquid phases, metastable with respect to a solid phase, form in solutions of proteins and small-molecule materials. They have been shown to serve as a prerequisite for the nucleation of crystals and other ordered solid phases. Here, using crystals of the protein lumazine synthase from Bacillus subtilis, which grow by the generation and spreading of layers, we demonstrate that within a range of supersaturations the only mechanism of generation of growth layers involves the association of submicrometer-size droplets of the dense liquid to the crystal surface. The dense liquid is metastable not only with respect to the crystals, but also with respect to the low-concentration solution: dynamic light scattering reveals that the droplets' lifetime is limited to several seconds, after which they decay into the low-concentration solution. The short lifetime does not allow growth to detectable dimensions so that liquid-liquid phase separation is not observed within a range of conditions broader than the one used for crystallization. If during their lifetime the droplets encounter a crystal surface, they lower their free energy not by decay, but by transformation into crystalline matter, ensuring perfect registry with the substrate. These observations illustrate two novel features of phase transformations in solutions: the existence of doubly metastable, short-lifetime dense phases and their crucial role for the growth of an ordered solid phase.

Stable equidistant step trains during crystallization of insulin.

Bunching of growth steps plagues layerwise crystallization of materials in laboratory, industrial, and geological environments, and theory predicts that equidistant step trains are unstable under a variety of conditions. Searching for an example of stable equidistant step trains, we monitored the generation and spatiotemporal evolution of step trains on length scales from 100 nm to 1 mm during the crystallization of insulin, using atomic force microscopy and phase-shifting interferometry. We show that near-equidistant step trains are generated by single and cooperating screw dislocation. The lack of step-step interaction and the overall transport-controlled growth regime further regularize the step train and ensure the stability of the obtained equidistant arrangement.

Diffusion-limited kinetics of the solution-solid phase transition of molecular substances.

For critical tests of whether diffusion-limited kinetics is an option for the solution-solid phase transition of molecular substances or whether they are determined exclusively by a transition state, we performed crystallization experiments with ferritin and apoferritin, a unique pair of proteins with identical shells but different molecular masses. We find that the kinetic coefficient for crystallization is identical (accuracy

Step bunching in a diffusion-controlled system: phase-shifting interferometry investigation of ferritin.

We present a novel phase-shifting interferometry technique for investigations of the unsteady kinetics and the formation of spatio-temporal patterns during the protein crystallization. We applied this technique to the ferritin crystal growth, which is controlled by the rate of supply of material. We find strong fluctuations of growth rate, step density and step velocity due to passage of step bunches. The fluctuation amplitudes decrease with higher supersaturation and larger crystal size, as well as with increasing distance from the step sources. Since these are parameters affecting the solute supply field, we conclude that fluctuations are rooted in the coupling of the interfacial processes of growth to the bulk transport in the solution. Analysis of the step velocity dependence on local slope indicates a very weak interaction between the steps. Hence, in diffusion-controlled systems with non-interacting or weakly interacting steps the stable growth mode is that via equidistant step trains, and randomly arising step bunches decay.