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DYNLRB1 is essential for dynein mediated transport and neuronal survival
Get PDFThe cytoplasmic dynein motor complex transports essential signals and organelles from the cell periphery to the perinuclear region, hence is critical for the survival and function of highly polarized cells such as neurons. Dynein Light Chain Roadblock-Type 1 (DYNLRB1) is thought to be an accessory subunit required for specific cargos, but here we show that it is essential for general dynein-mediated transport and sensory neuron survival. Homozygous Dynlrb1 null mice are not viable and die during early embryonic development. Furthermore, heterozygous or adult knockdown animals display reduced neuronal growth, and selective depletion of Dynlrb1 in proprioceptive neurons compromises their survival. Conditional depletion of Dynlrb1 in sensory neurons causes deficits in several signaling pathways, including beta-catenin subcellular localization, and a severe impairment in the axonal transport of both lysosomes and retrograde signaling endosomes. Hence, DYNLRB1 is an essential component of the dynein complex, and given dynein's critical functions in neuronal physiology, DYNLRB1 could have a prominent role in the etiology of human neurodegenerative diseases.journal articl
Chiral excitation of a single atom by a quantized single-photon pulse in a guided mode of a nanofiber
Get PDFWe study the interaction between a single two-level atom and a quantized single-photon probe pulse in a guided mode of a nanofiber. We examine the situation of chiral interaction, where the atom has a dipole rotating in the meridional plane of the nanofiber and the probe pulse is quasilinearly polarized along the radial direction of the atom position in the fiber transverse plane. We show that the atomic excitation probability, the photon transmission flux, and the photon transmission probability depend on the propagation direction of the probe pulse along the fiber axis. In contrast, the reflection flux and the reflection probability do not depend on the propagation direction of the probe pulse. We find that, unlike the atomic excitation probability, the asymmetry parameter for this characteristic does not vary in time and does not depend on the probe pulse shape.journal articl
Social tolerance in Octopus laqueus—A maximum entropy model
Get PDFOctopus laqueus is a small tropical octopus found in Okinawa, Japan and the greater Indo-Pacific. Octopus are often viewed as solitary animals but O. laqueus live in close proximity in the wild, and will potentially encounter one another on a regular basis, raising the possibility of social tolerance. Adopting shared den occupancy in aquaria as a potential measure of social tolerance in O. laqueus, we studied the animals’ preference for shared dens over solitude. We characterized dependence of sharing preference on sex, den availability and den occupancy density. We designed two simple social tolerance assays in aquaria with a total of 45 daily measurements: (i) Pots Equal, with equal numbers of octopuses and dens and (ii) Pots Limited, with a 3:1 ratio of octopuses to dens. We found that O. laqueus will socially tolerate other individuals by sharing tanks and dens and with typically no loss to cannibalism or escape. However, animals also exhibit significant levels of social repulsion, and individuals often chose a solitary den when given the option. The patterns of den occupancy are observed to be consistent with a maximum entropy model that balances seeking shelter against avoiding other animals. The model accurately captures and predicts the data and can be generalized to other organisms and their social interactions. Overall, in O. laqueus the preference for a den is stronger than the preference to be solitary. The animals are tolerant of others with a mixture of sizes in the tank and even in a den, a reported first for octopuses outside mating. The relaxed disposition and social tolerance of O. laqueus make it a promising species to work with in the lab to explore social and potentially other behaviors in octopuses.journal articl
Voltage Imaging of Cortical Oscillations in Layer 1 with Two-Photon Microscopy
Get PDFMembrane voltage oscillations in layer 1 (L1) of primary sensory cortices might be important indicators of cortical gain control, attentional focusing, and signal integration. However, electric field recordings are hampered by the low seal resistance of electrodes close to the brain surface. To study L1 membrane voltage oscillations, we synthesized a new voltage-sensitive dye, di1-ANNINE-6plus, that can diffuse into tissue. We applied it with a new surgery, leaving the dura intact but allowing injection of large quantities of staining solution, and imaged cortical membrane potential oscillations with two-photon microscopy depth-resolved (25 to 100 microm below dura) in anesthetized and awake mice. We found delta (0.5-4 Hz), theta (4-10 Hz), low beta (10-20 Hz), and low gamma (30-40 Hz) oscillations. All oscillations were stronger in awake animals. While the power of delta, theta, and low beta oscillations increased with depth, the power of low gamma was more constant throughout L1. These findings identify L1 as an important coordination hub for the dynamic binding process of neurons mediated by oscillations.journal articl
Scanning Tunneling Microscopy and Photoelectron Spectroscopy Studies of Lead Halide Perovskite Surfaces, Defect Dynamics and the MAPbX 3 - CuPc Interface
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyOver the past decade, lead halide perovskites (PVKs) have emerged as a promising new light absorber material for thin film solar cells. Lab-scale perovskite-based photovoltaic devices have made impressive gains in power conversion efficiency (PCE) and are nearing the same efficiency as silicon-based solar cells. However, perovskite solar cells lack stability, and this is a major obstacle preventing commercialization. The interfaces between the different layers in a device have been implicated as potential areas of charge recombination and material degradation. Understanding the perovskite surface is crucial because it is involved in these interfaces and also because it is the layer that is in first contact with extrinsic species that may cause degradation. Defects in the perovskite material have also been identified as a potential cause of sub-optimal performance. Additionally, some strategies for improving stability have included using mixed halide perovskites, or perovskites containing cesium instead of or mixed with organic cations such as methylammonium (MA). Reports at the device engineering level are plentiful, but fundamental, atomic-scale understanding of the perovskite surface is scarce, especially from an experimental perspective. This bulk of this thesis focuses on scanning tunneling microscopy (STM) studies examining the perovskite surfaces of CsPbBr₃ and mixed halide perovskites MAPbBr₃-yIy and MAPbBr₃-zClz, the surface defects of MAPbBr₃ and their dynamics, as well a device-relevant perovskite/hole transport material (HTM) interface comprised of MAPbX₃/CuPc, where X=I or Br. Furthermore, X-ray photoelectron spectroscopy (XPS) is used to characterize stability of the material, and electronic properties are investigated by ultraviolet photoemission spectroscopy (UPS). Where feasible, these experimental results are corroborated by density functional theory (DFT) calculations performed by collaborators. The goal of this thesis is to provide fundamental insight regarding perovskite surfaces, their defects and their dynamics, and their interfaces with other materials, which may help guide applied research toward creating devices with better performance and stability.doctoral thesi
Pycabnn: Efficient and Extensible Software to Construct an Anatomical Basis for a Physiologically Realistic Neural Network Model
Get PDFPhysiologically detailed models of neural networks are an important tool for studying how biophysical mechanisms impact neural information processing. An important, fundamental step in constructing such a model is determining where neurons are placed and how they connect to each other, based on known anatomical properties and constraints given by experimental data. Here we present an open-source software tool, pycabnn, that is dedicated to generating an anatomical model, which serves as the basis of a full network model. In pycabnn, we implemented efficient algorithms for generating physiologically realistic cell positions and for determining connectivity based on extended geometrical structures such as axonal and dendritic morphology. We demonstrate the capabilities and performance of pycabnn by using an example, a network model of the cerebellar granular layer, which requires generating more than half a million cells and computing their mutual connectivity. We show that pycabnn is efficient enough to carry out all the required tasks on a laptop computer within reasonable runtime, although it can also run in a parallel computing environment. Written purely in Python with limited external dependencies, pycabnn is easy to use and extend, and it can be a useful tool for computational neural network studies in the future.journal articl
Measurement of baseline locomotion and other behavioral traits in a common marmoset model of Parkinsonʼs disease established by a single administration regimen of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine
Get PDFBaseline locomotion and behavioral traits in the common marmoset Parkinson's disease model were examined to provide basic information for preclinical evaluations of medical treatments. A single regimen of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine at a cumulative dose of 5 mg/kg as the free base over three consecutive days was administered subcutaneously to 10 marmosets. Data obtained from these marmosets were compared to pre-1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine levels or 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine free marmosets. After the single regimen, reduced daily locomotion, a measure of immobility (a primary sign of Parkinsonism), was observed for more than a year. A moving tremor was also observed by visual inspection during this period. When apomorphine (0.13 mg/kg, s.c.) was administered, either right or left circling behavior was observed in a cylindrical chamber in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine marmosets, suggestive of unequal neural damage between the two brain hemispheres to different extents. MRI revealed that T1 relaxation time in the right substantia nigra correlated with right circling in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine marmosets. Histology was supportive of dopaminergic neural loss in the striatum. These results increase our understanding of the utility and limitations of the Parkinson's disease model in marmosets with a single 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine regimen, and provide reference data for efficacious preclinical evaluations.journal articl
Astrocyte calcium activity mapping in behaving mice using anterograde axo-astrocytic AAV transfer
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyAstrocytes are considered active partners to neurons in information processing. Heterogeneous, bidirectional interaction between neurons and astrocytes alludes to circuit specific communication. However, the role of astrocytes in information processing, primarily established through ex vivo experiments, has been challenged by a series of controversies that highlighted the importance of studying astrocytes under fully physiological conditions in behaving mice. Astrocytes extend highly ramified processes that cradle synapses. They form functionally independent microdomains where they exhibit a rich repertoire of localized calcium signals. How astrocyte Ca²+ microdomain signals relate to neuronal activity and behaviour in vivo is still unclear. My objective was to investigate circuit specific, single-astrocyte Ca²+ microdomain activity in mice during behavioural states and sensory stimuli. I found that adeno-associated viruses (AAVs) can transfer anterogradely along thalamocortical projections to transduce cortical astrocytes and neurons. This axo-astrocytic AAV transfer enables the study of astrocytes and neurons embedded in specific neuronal circuits. Intersectional approaches, using anterograde axo-astrocytic AAV transfer in combination with membrane tagged genetically encoded calcium indicators (GECIs), enabled sparse, high contrast labelling of cortical astrocytes embedded in the somatosensory system of mice. Continuous imaging with two-photon microscopy of single astrocytes for about ≈1 hour combined with automatic, unbiased extraction of Ca²+ activity revealed a rich repertoire of subsecond, µm scale, localized Ca²+ signals. The number, size and duration of astrocytic Ca²+ signals were modulated with locomotion but not with intermittent whisker-touch stimulation. Locomotion and whisker stimuli evoked rapid [Ca²+]i elevation in thalamocortical axon boutons, whose activity was not correlated with nearby astrocyte Ca²+ microdomain signalling. Astrocyte fine processes exhibit heterogeneous, non-random, Ca²+ signalling patterns giving rise to hotspots of higher activity that are stable over time. Hotspot patterns allude to subcellular specialization. Our study: a) provides a new toolkit for studying neuron-astrocyte interactions within brain circuits, b) extends our understanding of astrocyte Ca²+ microdomain signalling and relationship to neuronal activity in behaving animals and c) suggests that there are astrocyte Ca²+ activity maps in the brain.doctoral thesi
An Epigenetic Signature for Within-Generational Plasticity of a Reef Fish to Ocean Warming
Get PDFElevated temperature can have detrimental effects on the physiological performance of many marine organisms. However, phenotypic plasticity may enable some populations to maintain their performance under thermal stress. Two longitudinally separated populations of the coral reef fish, Acanthochromis polyacanthus from the Great Barrier Reef have shown differing capacities for thermal plasticity - the southernmost Heron Island population restored aerobic scope within one generation at a higher temperature, whereas the northernmost Palm Island population restored aerobic scope only when two generations were exposed to warmer conditions. We recently discovered an epigenetic signature associated with transgenerational plasticity in the Palm Island population. Here, we aimed to determine if epigenetic changes are also associated with the within-generational plasticity observed in the Heron Island population and, if so, how this epigenetic signature compares to the Palm Island transgenerational epigenome. By sequencing and analyzing the genome-wide DNA methylome of fish reared at control (+0 degrees C) or elevated temperatures (+1.5 and +3 degrees C) since early life, we identified 480 differentially methylated genomic regions and 372 adjacent protein-coding genes associated with within-generational plasticity in the Heron Island population. Functions related to insulin, cardiovascular capacity, development, and heat response were significantly enriched in differentially methylated genes, suggesting that these functions are the core mechanisms for within-generational restoration of aerobic scope. Comparison to the differentially methylated genes identified from F2 Palm Island population revealed little overlap of genes and enriched functions, indicating that distinct genetic toolkits may be used for within- and between-generational plasticity to ocean warming in the same species from different latitudes.journal articl
Metabolic engineering of a novel strain of electrogenic bacterium Arcobacter butzleri to create a platform for single analyte detection using a microbial fuel cell
Get PDFElectrogenic bacteria metabolize organic substrates by transferring electrons to the external electrode, with subsequent electricity generation. In this proof-of-concept study, we present a novel strain of a known, electrogenic Arcobacter butzleri that can grow primarily on acetate and lactate and its electric current density is positively correlated (R(2)=0.95) to the COD concentrations up to 200ppm. Using CRISPR-Cas9 and Cpf1, we engineered knockout Arcobacter butzleri mutants in either the acetate or lactate metabolic pathway, limiting their energy metabolism to a single carbon source. After genome editing, the expression of either acetate kinase, ackA, or lactate permease, lctP, was inhibited, as indicated by qPCR results. All mutants retain electrogenic activity when inoculated into a microbial fuel cell, yielding average current densities of 81-82mA/m(2), with wild type controls reaching 85-87mA(2). In the case of mutants, however, current is only generated in the presence of the substrate for the remaining pathway. Thus, we demonstrate that it is possible to obtain electric signal corresponding to the specific organic compound via genome editing. The outcome of this study also indicates that the application of electrogenic bacteria can be expanded by genome engineering.journal articl