Fraping: A computational tool for detecting slight differences in fluorescence recovery after photobleaching (FRAP) data for actin polymerization analysis.

Fluorescence recovery after photobleaching (FRAP) is a laser method of light microscopy to evaluate the rapid movement of fluorescent molecules. To have a more reliable approach to analyze data from FRAP, we designed Fraping, a free access R library to data analysis obtained from FRAP. Unlike other programs, Fraping has a new form of analyzing curves of FRAP using statistical analysis based on the average curve difference. To evaluate our library, we analyzed the differences of actin polymerization in real time between dendrites and secondary neurites of cultured neuron transfected with LifeAct to track F-actin changes of neurites. We found that Fraping provided greater sensitivity than the conventional model using mobile fraction analysis. Likewise, this approach allowed us to normalize the fluorescence to the size area of interest and adjust data curves choosing the best parametric model. In addition, this library was supplemented with data simulation to have a more significant enrichment for the analysis behavior. We concluded that Fraping is a method that reduces bias when analyzing two data groups as compared with the conventional methods. This method also allows the users to choose a more suitable analysis approach according to their requirements. RESEARCH HIGHLIGHTS: Fraping is a new programming tool to analyze FRAP data to normalize fluorescence recovery curves. The conventional method uses one-point analysis, and the new one compares all the points to define the similarity of the fluorescence recovery.

Self assembling cluster crystals from DNA based dendritic nanostructures.

Cluster crystals are periodic structures with lattice sites occupied by several, overlapping building blocks, featuring fluctuating site occupancy, whose expectation value depends on thermodynamic conditions. Their assembly from atomic or mesoscopic units is long-sought-after, but its experimental realization still remains elusive. Here, we show the existence of well-controlled soft matter cluster crystals. We fabricate dendritic-linear-dendritic triblock composed of a thermosensitive water-soluble polymer and nanometer-scale all-DNA dendrons of the first and second generation. Conclusive small-angle X-ray scattering (SAXS) evidence reveals that solutions of these triblock at sufficiently high concentrations undergo a reversible phase transition from a cluster fluid to a body-centered cubic (BCC) cluster crystal with density-independent lattice spacing, through alteration of temperature. Moreover, a rich concentration-temperature phase diagram demonstrates the emergence of various ordered nanostructures, including BCC cluster crystals, birefringent cluster crystals, as well as hexagonal phases and cluster glass-like kinetically arrested states at high densities.

Self-Assembly of Dendritic DNA into a Hydrogel: Application in Three-Dimensional Cell Culture.

With inherent biocompatibility, biodegradability, and unique programmability, hydrogels with a DNA framework show great potential in three-dimensional (3D) cell culture. Here, a DNA hydrogel was assembled by a dendritic DNA with four branches. The hydrogel showed tunable mechanical strength and reversible thixotropy even under a nanomolar DNA concentration. The cell culture medium can be converted into the hydrogel isothermally at physiological temperature. This DNA hydrogel allows both cancer and somatic cells to be seeded in situ and to achieve high proliferation and viability. The bis-entity of dendritic branches enabled the specific loading of bioactive clues to regulate cell behaviors. Thus, the dendritic DNA-assembled hydrogel could serve as a highly biocompatible, readily functionalizing, and easy-casting gel platform for 3D cell culture.

Characterization of Tbr2-expressing retinal ganglion cells.

The mammalian retina contains more than 40 retinal ganglion cell (RGC) subtypes based on their unique morphologies, functions, and molecular profiles. Among them, intrinsically photosensitive RGCs (ipRGCs) are the first specified RGC type emerging from a common retinal progenitor pool during development. Previous work has shown that T-box transcription factor T-brain 2 (Tbr2) is essential for the formation and maintenance of ipRGCs, and that Tbr2-expressing RGCs activate Opn4 expression upon native ipRGC ablation, suggesting that Tbr2+ RGCs contain a reservoir for ipRGCs. However, the identity of Tbr2+ RGCs has not been fully vetted. Here, using genetic sparse labeling and single cell recording, we showed that Tbr2-expressing retinal neurons include RGCs and a subset of GABAergic displaced amacrine cells (dACs). Most Tbr2+ RGCs are intrinsically photosensitive and morphologically resemble native ipRGCs with identical retinofugal projections. Tbr2+ RGCs also include a unique and rare Pou4f1-expressing OFF RGC subtype. Using a loss-of-function strategy, we have further demonstrated that Tbr2 is essential for the survival of these RGCs and dACs, as well as maintaining the expression of Opn4. These data set a strong foundation to study how Tbr2 regulates ipRGC development and survival, as well as the expression of molecular machinery regulating intrinsic photosensitivity.

Nectin-2α is localized at cholinergic neuron dendrites and regulates synapse formation in the medial habenula.

The medial habenula (MHb) receives afferents from the triangular septum and the medial septal complex, projects efferents to the interpeduncular nucleus (IPN) in the midbrain to regulate dopamine and serotonin levels, and is implicated in stress, depression, memory, and nicotine withdrawal syndrome. We previously showed that the cell adhesion molecule nectin-2α is localized at the boundary between adjacent somata of clustered cholinergic neurons and regulates the voltage-gated A-type K+ channel Kv4.2 localization at membrane specializations in the MHb. This adhesion apparatus, named nectin-2α spots, is not associated with the nectin-binding protein afadin or any classic cadherins and their binding proteins p120-catenin and ß-catenin. We showed here that nectin-2α was additionally localized at cholinergic neuron dendrites in synaptic regions of the MHb. The genetic ablation of nectin-2 reduced the number of synapses in the MHb without affecting their morphology. Nectin-2α was associated with afadin, cadherin-8, p120-catenin, ß-catenin, and αN-catenin, forming puncta adherentia junctions (PAJs). Nectin-2α was observed in the IPN, but not in the triangular septum or the medial septal complex. The genetic ablation of nectin-2 did not affect synapse formation in the IPN. These results indicate that nectin-2α forms two types of adhesion apparatus in the MHb, namely nectin-2α spots at neighboring somata and PAJs at neighboring dendrites, and that dendritic PAJs regulate synapse formation in the MHb.

Immunizing lithium metal anodes against dendrite growth using protein molecules to achieve high energy batteries.

The practical applications of lithium metal anodes in high-energy-density lithium metal batteries have been hindered by their formation and growth of lithium dendrites. Herein, we discover that certain protein could efficiently prevent and eliminate the growth of wispy lithium dendrites, leading to long cycle life and high Coulombic efficiency of lithium metal anodes. We contend that the protein molecules function as a "self-defense" agent, mitigating the formation of lithium embryos, thus mimicking natural, pathological immunization mechanisms. When added into the electrolyte, protein molecules are automatically adsorbed on the surface of lithium metal anodes, particularly on the tips of lithium buds, through spatial conformation and secondary structure transformation from α-helix to ß-sheets. This effectively changes the electric field distribution around the tips of lithium buds and results in homogeneous plating and stripping of lithium metal anodes. Furthermore, we develop a slow sustained-release strategy to overcome the limited dispersibility of protein in the ether-based electrolyte and achieve a remarkably enhanced cycling performance of more than 2000 cycles for lithium metal batteries.

An important role of PHRF1 in dendritic architecture and memory formation by modulating TGF-ß signaling.

PHRF1 is involved in transforming growth factor ß (TGF-ß) signaling to constrain the formation of acute promyelocytic leukemia (APL) in mouse APL models. PHRF1 also participates in modulating non-homologous end-joining. However, the role of PHRF1 in mammalian dendrite architecture and synaptic plasticity is unclear. Here, we investigated the role of PHRF1 in dendritic formation in the murine hippocampus using Camk2a promoter driven-iCre recombinase to conduct a PHRF1 conditional knockout, namely PHRF1Δ/Δ, in the forebrain region. PHRF1Δ/Δ mice developed normally, but exhibited anxiety-like behaviors and displayed defective spatial memory. Alterations of dendritic complexity in apical and basal dendrites of pyramidal neurons were noticed in PHRF1Δ/Δ mutants. Furthermore, electrical stimulation in the hippocampal CA1 region after the TGF-ß1 treatment showed a reduced synaptic plasticity in PHRF1Δ/Δ mice. Immunoblotting analysis indicated that PHRF1 ablation affected the TGF-ß signaling. Collectively, our results demonstrate that PHRF1 is important for the dendritic architecture and required for spatial memory formation in the hippocampus.

Banana Peel-Derived Dendrite-Shaped Au Nanomaterials with Dual Inhibition Toward Tumor Growth and Migration.

PURPOSE: In order to prepare functional Au nanoparticles with low toxicity and high antitumor properties, we have used fruit waste (banana peel) to synthesize a new dendrite-shaped gold nanoparticle and used it for the treatment of tumors. METHODS: Dendrite-shaped gold nanoparticle (Au-dendrite) was synthesized through a facile hydrothermal process. The banana peel was used as both the reducing agent and the protective agent for reducing chloroauric acid to obtain Au-dendrite. The safety assessment of the Au-dendrite was conducted by H&E staining of the mouse's eyelid skin and CCK-8 assay. The antitumor effects were evaluated through in vitro tumor cytotoxicity experiments and in vivo treatment of animal tumors. RESULTS: In this work, a new type of gold nanomaterial (Au-dendrite) was synthesized by using a common agricultural waste (banana peel) through a facile hydrothermal process without any extra chemical reducing agent or protective agent. Subsequent experiments showed that, compared with some classical Au nanomaterials, the as-synthesized gold nanocomposites have superior biocompatibility and impressive characteristics of dual inhibition toward tumor growth and migration. CONCLUSION: We successfully synthesized a dendrite-shaped gold nanocomposite which was derived from a common agricultural waste (banana peel). A facile and environmentally friendly synthetic process was proposed accordingly without regular chemical additives. The as-prepared Au-dendrite nanocomposites not only had better biocompatibility than some classical gold nanoparticles but also exhibited unique advantages in tumor inhibition.

Dynamic compartmentalization of calcium channel signalling in neurons.

Calcium fluxes through the neuronal membrane are strictly limited in time due to biophysical properties of voltage-gated and ligand-activated ion channels and receptors. Being embedded into the crowded dynamic environment of biological membranes, Ca2+-permeable receptors and channels undergo perpetual spatial rearrangement, which enables their temporary association and formation of transient signalling complexes. Thus, efficient calcium-mediated signal transduction requires mechanisms to support very precise spatiotemporal alignment of the calcium source and Ca2+-binding lipids and proteins in a highly dynamic environment. The mobility of calcium channels and calcium-sensing proteins themselves can be considered as a physiologically meaningful variable that affects calcium-mediated signalling in neurons. In this review, we will focus on voltage-gated calcium channels (VGCCs) and activity-induced relocation of stromal interaction molecules (STIMs) in the endoplasmic reticulum (ER) to show that particularly in time ranges between milliseconds to minutes, dynamic rearrangement of calcium conducting channels and sensor molecules is of physiological relevance. This article is part of the special issue entitled 'Mobility and trafficking of neuronal membrane proteins'.

Effect of heat treatment on the bio-corrosion properties and wear resistance of antibacterial Co-29Cr-6Mo-xCu alloys.

Co-Cr-Mo alloys have been widely used in hip implants due to their good corrosion resistance and good wear resistance. However, complaint is still raising due to infection and inflammation. The addition of Cu has been proven to be an effective way to develop a new kind of Co-based alloy with good antibacterial properties. In this paper, the effect of heat treatment on the corrosion property, the tribology property and the antibacterial property of Cu containing Co-based alloys were investigated in detail. The microstructure observation showed that the as-cast alloys mainly consisted of a dendritic matrix with carbide dispersion at grain boundaries and a fine Cu-rich phase in the matrix and at the carbide/matrix interface. The carbide precipitates and the distribution of Cu phases affected significantly the friction coefficient and wear resistance of Co-xCu alloy. Annealing at 1060 °C/24 h promoted the precipitation of carbide and in turn increased the hardness and wear resistance markedly. Heat treatments, including annealing, solid solution and ageing treatment, enhanced the corrosion resistance of Co-xCu alloy without reduction in antibacterial properties. However, the addition of Cu increased the corrosion resistance and antibacterial properties but reduced the wear resistance especially at high Cu content.

Axonal projection-specific differences in somatodendritic α2 autoreceptor function in locus coeruleus neurons.

The locus coeruleus (LC) contains the majority of central noradrenergic neurons sending wide projections throughout the entire CNS. The LC is considered to be essential for multiple key brain functions including arousal, attention and adaptive stress responses as well as higher cognitive functions and memory. Electrophysiological studies of LC neurons have identified several characteristic functional features such as low-frequency pacemaker activity with broad action potentials, transient high-frequency burst discharges in response to salient stimuli and an apparently homogeneous inhibition of firing by activation of somatodendritic α2 autoreceptors (α2AR). While stress-mediated plasticity of the α2AR response has been described, it is currently unclear whether different LC neurons projecting to distinct axonal targets display differences in α2AR function. Using fluorescent beads-mediated retrograde tracing in adult C57Bl6/N mice, we compared the anatomical distributions and functional in vitro properties of identified LC neurons projecting either to medial prefrontal cortex, hippocampus or cerebellum. The functional in vitro analysis of LC neurons confirmed their mostly uniform functional properties regarding action potential generation and pacemaker firing. However, we identified significant differences in tonic and evoked α2AR-mediated responses. While hippocampal-projecting LC neurons were partially inhibited by endogenous levels of norepinephrine and almost completely silenced by application of saturating concentrations of the α2 agonist clonidine, prefrontal-projecting LC neurons were not affected by endogenous levels of norepinephrine and only partially inhibited by saturating concentrations of clonidine. Thus, we identified a limited α2AR control of electrical activity for prefrontal-projecting LC neurons indicative of functional heterogeneity in the LC-noradrenergic system.

Dendritic core-shell rhodium@platinum-cobalt nanocrystals for ultrasensitive electrochemical immunoassay of squamous cell carcinoma antigen.

Squamous cell carcinoma antigen (SCCA) has great diagnostic values for its high specificity (90-96%) in diagnosis of squamous cell carcinoma especially cancers, where electrochemical immunoassay is powerful for its accurate and reliable detection of specific tumor biomarkers at very low levels. In this work, well-defined three-dimensional dendritic core-shell rhodium@platinum-cobalt nanocrystals (Rh@PtCo NCs) were facilely prepared via a simple one-pot solvothermal strategy. Taking advantage of dramatically enhanced catalytic activity of the Rh@PtCo NCs for catechol oxidation, a label-free electrochemical immunosensor was developed for highly sensitive assay of SCCA. Under optimal conditions, the electrochemical signals were linearly correlated with the logarithm of the SCCA concentration, showing a broad linear range from 0.0001 to 10.0 ng mL-1 and a ultralow detection limit of 0.04 pg mL-1 (S/N = 3). The resultant immunosensor was further exploited for actual analysis of serum samples with convinced results. This immunosensor has good expectation in actual samples analysis and provides a universal approach for detection of other tumor markers and disease surveillance.

Golgi-Cox Staining of Neuronal Dendrites and Dendritic Spines With FD Rapid GolgiStain™ Kit.

The Golgi-Cox method has been one of the most effective techniques for studying the morphology of neuronal dendrites and dendritic spines. However, the reliability and time-consuming process of Golgi-Cox staining have been major obstacles to the widespread application of this technique. To overcome these shortcomings and to promote this invaluable technique, we developed the FD Rapid GolgiStain™ Kit based on the principle of the methods described by Ramón-Moliner in 1970 and Glaser and Van der Loos in 1981. The kit significantly improves and simplifies the Golgi-Cox technique. This kit is reliable for visualizing morphological details of neurons, allowing for analysis of various parameters of dendritic morphology-such as dendritic length and branching pattern and dendritic spine number, shape, and size-in both animal and postmortem human brains. A 40-min instructional video for tissue freezing, cryosectioning, and staining is provided. © 2019 by John Wiley & Sons, Inc.

Dynamic super-resolution structured illumination imaging in the living brain.

Cells in the brain act as components of extended networks. Therefore, to understand neurobiological processes in a physiological context, it is essential to study them in vivo. Super-resolution microscopy has spatial resolution beyond the diffraction limit, thus promising to provide structural and functional insights that are not accessible with conventional microscopy. However, to apply it to in vivo brain imaging, we must address the challenges of 3D imaging in an optically heterogeneous tissue that is constantly in motion. We optimized image acquisition and reconstruction to combat sample motion and applied adaptive optics to correcting sample-induced optical aberrations in super-resolution structured illumination microscopy (SIM) in vivo. We imaged the brains of live zebrafish larvae and mice and observed the dynamics of dendrites and dendritic spines at nanoscale resolution.

RNA-mediated, green synthesis of palladium nanodendrites for catalytic reduction of nitroarenes.

Palladium (Pd)-catalyzed reactions mostly show structure sensitivity: i.e., the selectivity and activity of the reactions are highly dependent on the arrangement of Pd atoms. In this regard, branched Pd nanoparticles show enhanced catalytic performance owing to the presence of low coordinated Pd atoms. In this paper, a novel solution-phase synthesis of flower-like Pd nanodendrites using ribonucleic acid (RNA) as a capping agent and ascorbic acid as a reducing agent was described. On the other hand, the co-use of polyvinylpyrrolidone (PVP) and potassium bromide (KBr) instead of RNA at the same synthesis conditions led to cuboid nanoparticles, while the sole use of ascorbic acid resulted in faceted nanoparticles. The formation of nanodendritic morphology was attributed to the RNA-assisted growth through particle attachment. This scenario was supported by TEM analysis that demonstrated the aggregation of small particles to form larger nanoparticles at the onset of the reaction. The shape and size of the nanoparticles could be readily tuned by the RNA content used. XPS confirmed the formation of metallic Pd nanoparticles. The presence of crystalline planes of {1 1 1}, {2 0 0}, {2 2 0}, {3 1 1} and {2 2 2} was demonstrated by XRD and SAED analyses. The Pd nanodendrites were used for the reduction of p-nitrophenol (PNP) and 2,4,6-trinitrotoluene (TNT), and reduction rate constants (k) were calculated as 1.078 min-1 (normalized rate constant, knor = 59.66 mmol-1 s-1) for PNP and 0.3181 min-1 (knor = 17.6 mmol-1 s-1) for TNT with the corresponding turnover frequencies (TOFs) as 16.06 and 40.80 h-1, respectively.

Sestd1 Encodes a Developmentally Dynamic Synapse Protein That Complexes With BCR Rac1-GAP to Regulate Forebrain Dendrite, Spine and Synapse Formation.

SEC14 and Spectrin domain-1 (Sestd1) is a synapse protein that exhibits a striking shift from the presynaptic to postsynaptic space as neurons mature postnatally in the mouse hippocampus. Hippocampal pyramidal neurons from mice with global genetic deletion of Sestd1 have reduced dendrite arbors, spines, and excitatory synapses. Electrophysiologically this correlates with cell-autonomous reductions in both AMPA- and NMDA-excitatory postsynaptic currents in individual hippocampal neurons from which Sestd1 has been deleted in vivo. These neurodevelopmental and functional deficits are associated with increased activation of the Rho family GTPases Rac1 and RhoA. Co-immunoprecipitation and mass spectrometry reveal that the Breakpoint Cluster Region protein, a Rho GTPase activating protein (GAP), forms complexes with Sestd1 in brain tissue. This complements earlier findings that Sestd1 can also partner with other Rho family GAPs and guanine nucleotide exchange factors. Our findings demonstrate that Sestd1 is a developmentally dynamic synaptic regulator of Rho GTPases that contributes to dendrite and excitatory synapse formation within differentiating pyramidal neurons of the forebrain.

Towards a supervised classification of neocortical interneuron morphologies.

BACKGROUND: The challenge of classifying cortical interneurons is yet to be solved. Data-driven classification into established morphological types may provide insight and practical value. RESULTS: We trained models using 217 high-quality morphologies of rat somatosensory neocortex interneurons reconstructed by a single laboratory and pre-classified into eight types. We quantified 103 axonal and dendritic morphometrics, including novel ones that capture features such as arbor orientation, extent in layer one, and dendritic polarity. We trained a one-versus-rest classifier for each type, combining well-known supervised classification algorithms with feature selection and over- and under-sampling. We accurately classified the nest basket, Martinotti, and basket cell types with the Martinotti model outperforming 39 out of 42 leading neuroscientists. We had moderate accuracy for the double bouquet, small and large basket types, and limited accuracy for the chandelier and bitufted types. We characterized the types with interpretable models or with up to ten morphometrics. CONCLUSION: Except for large basket, 50 high-quality reconstructions sufficed to learn an accurate model of a type. Improving these models may require quantifying complex arborization patterns and finding correlates of bouton-related features. Our study brings attention to practical aspects important for neuron classification and is readily reproducible, with all code and data available online.

Wnt signalling in the development of axon, dendrites and synapses.

Wnts are a highly conserved family of secreted glycoproteins that play essential roles in the morphogenesis and body patterning during the development of metazoan species. In recent years, mounting evidence has revealed important functions of Wnt signalling in diverse aspects of neural development, including neuronal polarization, guidance and branching of the axon and dendrites, as well as synapse formation and its structural remodelling. In contrast to Wnt signalling in cell proliferation and differentiation, which mostly acts through ß-catenin-dependent pathways, Wnts engage a diverse array of non-transcriptional cascades in neuronal development, such as the planar cell polarity, cytoskeletal or calcium signalling pathways. In this review, we summarize recent advances in the mechanisms of Wnt signalling in the development of axon, dendrite and synapse formation.

Learning-Related Plasticity in Dendrite-Targeting Layer 1 Interneurons.

A wealth of data has elucidated the mechanisms by which sensory inputs are encoded in the neocortex, but how these processes are regulated by the behavioral relevance of sensory information is less understood. Here, we focus on neocortical layer 1 (L1), a key location for processing of such top-down information. Using Neuron-Derived Neurotrophic Factor (NDNF) as a selective marker of L1 interneurons (INs) and in vivo 2-photon calcium imaging, electrophysiology, viral tracing, optogenetics, and associative memory, we find that L1 NDNF-INs mediate a prolonged form of inhibition in distal pyramidal neuron dendrites that correlates with the strength of the memory trace. Conversely, inhibition from Martinotti cells remains unchanged after conditioning but in turn tightly controls sensory responses in NDNF-INs. These results define a genetically addressable form of dendritic inhibition that is highly experience dependent and indicate that in addition to disinhibition, salient stimuli are encoded at elevated levels of distal dendritic inhibition. VIDEO ABSTRACT.

Tropomodulin Isoform-Specific Regulation of Dendrite Development and Synapse Formation.

Neurons of the CNS elaborate highly branched dendritic arbors that host numerous dendritic spines, which serve as the postsynaptic platform for most excitatory synapses. The actin cytoskeleton plays an important role in dendrite development and spine formation, but the underlying mechanisms remain incompletely understood. Tropomodulins (Tmods) are a family of actin-binding proteins that cap the slow-growing (pointed) end of actin filaments, thereby regulating the stability, length, and architecture of complex actin networks in diverse cell types. Three members of the Tmod family, Tmod1, Tmod2, and Tmod3 are expressed in the vertebrate CNS, but their function in neuronal development is largely unknown. In this study, we present evidence that Tmod1 and Tmod2 exhibit distinct roles in regulating spine development and dendritic arborization, respectively. Using rat hippocampal tissues from both sexes, we find that Tmod1 and Tmod2 are expressed with distinct developmental profiles: Tmod2 is expressed early during hippocampal development, whereas Tmod1 expression coincides with synaptogenesis. We then show that knockdown of Tmod2, but not Tmod1, severely impairs dendritic branching. Both Tmod1 and Tmod2 are localized to a distinct subspine region where they regulate local F-actin stability. However, the knockdown of Tmod1, but not Tmod2, disrupts spine morphogenesis and impairs synapse formation. Collectively, these findings demonstrate that regulation of the actin cytoskeleton by different members of the Tmod family plays an important role in distinct aspects of dendrite and spine development.SIGNIFICANCE STATEMENT The Tropomodulin family of molecules is best known for controlling the length and stability of actin myofilaments in skeletal muscles. While several Tropomodulin members are expressed in the brain, fundamental knowledge about their role in neuronal function is limited. In this study, we show the unique expression profile and subcellular distribution of Tmod1 and Tmod2 in hippocampal neurons. While both Tmod1 and Tmod2 regulate F-actin stability, we find that they exhibit isoform-specific roles in dendrite development and synapse formation: Tmod2 regulates dendritic arborization, whereas Tmod1 is required for spine development and synapse formation. These findings provide novel insight into the actin regulatory mechanisms underlying neuronal development, thereby shedding light on potential pathways disrupted in a number of neurological disorders.