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"Long, Brian"
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Spatially resolved transcriptomics in neuroscience
One major challenge in neuroscience is to gain a systematic understanding of the extraordinary diversity of brain cell types and how they contribute to brain function. Spatially resolved transcriptomics holds unmatched promise in unraveling the organization of brain cell types and their relationship with connectivity, circuit dynamics, behavior and disease. Here we discuss neuroscience applications of various spatially resolved transcriptomics methods, as well as technical challenges that need to be overcome to realize their full potentials.
Journal Article
Non–linear bonding trends in maleonitrile-1,2–dithiolate complexes of the transuranium actinides
The trivalent actinides are produced in the nuclear fuel cycle during power production and provide the largest long-term radiation dose in used nuclear fuel. It is ideal for these elements to be removed from used nuclear fuel for disposal and a necessity for fuel recycling. A key challenge to this is the similarity of chemical behavior of the trivalent actinides to the lanthanides that are also present as fission products in used fuel. Thus far, some of the most effective separations of actinides from lanthanides utilise chelating agents containing sulfur moieties such as dithiophosphinates that selectively bind to actinide ions because of a greater bond covalency relative to lanthanide ions. Typically, greater differences between actinide and lanthanide ions are observable the more ligands and chelators bonds have a covalent character. Here, a series of complexes of the trivalent actinides Np(III) through Cf(III) (excluding Bk(III)) with maleonitrile-1,2-dithiolate (mnt
2–
) are synthesized along with their lanthanide counterparts (La(III) – Nd(III), Sm(III) – Gd(III), Dy(III)), in order to characterize the nature of chemical bonds with these metal ions and a polarizable, non-innocent, sulfur-donor ligand. The metal-sulfur bonds in these complexes trend shorter than measured for lanthanides with equivalent ionic radii. However, particularly large deviations are observed in the neptunium and plutonium complexes in both structure and bonding, resulting in a nonlinear bond length trendline for the actinide series. Density Functional Theory (DFT) calculations with Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Order (NBO) analyses indicate that for the neptunium and plutonium complexes, the presence of increased 5
f
-orbital participation, energy degeneracy of the metal and ligand orbitals, and the structure packing result in shortened M–S bonds. The stabilization of the energy of the 5
f
-orbitals and the decrease in
f
-contribution to bonding orbitals in the later actinides results in structural properties more similar to the lanthanide complexes.
Although the trivalent actinides are similar to the lanthanide series in terms of chemistry and bonding, their structures and properties can diverge significantly. Here, the authors report a series of complexes of the trivalent actinides Np(III) through Cf(III) along with their lanthanide counterparts using a polarizable non-innocent, sulfur-donor ligand.
Journal Article
A comprehensive thalamocortical projection map at the mesoscopic level
In this resource, the authors provide a comprehensive map of the thalamocortical projections in the mouse brain. To do this, they employed 254 highly overlapping injections of viral vectors to label and characterize long-range projections. Using this map as a framework, the authors determine the functionality of a subset of these connections via expression and activation of channelrhodopsin.
The thalamus relays sensori-motor information to the cortex and is an integral part of cortical executive functions. The precise distribution of thalamic projections to the cortex is poorly characterized, particularly in mouse. We employed a systematic, high-throughput viral approach to visualize thalamocortical axons with high sensitivity. We then developed algorithms to directly compare injection and projection information across animals. By tiling the mouse thalamus with 254 overlapping injections, we constructed a comprehensive map of thalamocortical projections. We determined the projection origins of specific cortical subregions and verified that the characterized projections formed functional synapses using optogenetic approaches. As an important application, we determined the optimal stereotaxic coordinates for targeting specific cortical subregions and expanded these analyses to localize cortical layer–preferential projections. This data set will serve as a foundation for functional investigations of thalamocortical circuits. Our approach and algorithms also provide an example for analyzing the projection patterns of other brain regions.
Journal Article
Altering the spectroscopy, electronic structure, and bonding of organometallic curium(III) upon coordination of 4,4′−bipyridine
Structural and electronic characterization of (Cp′
3
Cm)
2
(
μ
−4,4′−bpy) (Cp′ = trimethylsilylcyclopentadienyl, 4,4′−bpy = 4,4′−bipyridine) is reported and provides a rare example of curium−carbon bonding. Cp′
3
Cm displays unexpectedly low energy emission that is quenched upon coordination by 4,4′−bipyridine. Electronic structure calculations on Cp′
3
Cm and (Cp′
3
Cm)
2
(
μ
−4,4′−bpy) rule out significant differences in the emissive state, rendering 4,4′−bipyridine as the primary quenching agent. Comparisons of (Cp′
3
Cm)
2
(
μ
−4,4′−bpy) with its samarium and gadolinium analogues reveal atypical bonding patterns and electronic features that offer insights into bonding between carbon with
f
-block metal ions. Here we show the structural characterization of a curium−carbon bond, in addition to the unique electronic properties never before observed in a curium compound.
Despite the distinct electronic properties of the wide variety Cm3+ compounds that have been prepared to date, no singlecrystal structural characterization of a complex containing a Cm−C bond has been reported. Here the authors report the synthesis of a Cm complex bearing trimethylsilylcyclopentadienyl and 4,4’-bipyridine ligands with a low energy emission and identify the 4,4’-bipyridine ligand as the primary quenching agent.
Journal Article
Cell segmentation-free inference of cell types from in situ transcriptomics data
Multiplexed fluorescence in situ hybridization techniques have enabled cell-type identification, linking transcriptional heterogeneity with spatial heterogeneity of cells. However, inaccurate cell segmentation reduces the efficacy of cell-type identification and tissue characterization. Here, we present a method called Spot-based Spatial cell-type Analysis by Multidimensional mRNA density estimation (SSAM), a robust cell segmentation-free computational framework for identifying cell-types and tissue domains in 2D and 3D. SSAM is applicable to a variety of in situ transcriptomics techniques and capable of integrating prior knowledge of cell types. We apply SSAM to three mouse brain tissue images: the somatosensory cortex imaged by osmFISH, the hypothalamic preoptic region by MERFISH, and the visual cortex by multiplexed smFISH. Here, we show that SSAM detects regions occupied by known cell types that were previously missed and discovers new cell types.
Inaccurate cell segmentation has been the major problem for cell-type identification and tissue characterization of the in situ spatially resolved transcriptomics data. Here we show a robust cell segmentation-free computational framework (SSAM), for identifying cell types and tissue domains in 2D and 3D.
Journal Article
Isolation of a californium(II) crown–ether complex
The actinides, from californium to nobelium (Z = 98–102), are known to have an accessible +2 oxidation state. Understanding the origin of this chemical behaviour requires characterizing CfII materials, but investigations are hampered by the fact that they have remained difficult to isolate. This partly arises from the intrinsic challenges of manipulating this unstable element, as well as a lack of suitable reductants that do not reduce CfIII to Cf°. Here we show that a CfII crown–ether complex, Cf(18-crown-6)I2, can be prepared using an Al/Hg amalgam as a reductant. Spectroscopic evidence shows that CfIII can be quantitatively reduced to CfII, and rapid radiolytic re-oxidation in solution yields co-crystallized mixtures of CfII and CfIII complexes without the Al/Hg amalgam. Quantum-chemical calculations show that the Cf‒ligand interactions are highly ionic and that 5f/6d mixing is absent, resulting in weak 5f→5f transitions and an absorption spectrum dominated by 5f→6d transitions.Californium is difficult to prepare in its divalent state. Now, crystals of a Cf(II) crown–ether complex have been synthesized by reduction of a Cf(III) precursor with an Al/Hg amalgam. They exhibit 5f→6d transitions in the visible region and near-infrared emission that are highly sensitive to changes in the coordination environment.
Journal Article
Cyclopentadienyl coordination induces unexpected ionic Am−N bonding in an americium bipyridyl complex
Variations in bonding between trivalent lanthanides and actinides is critical for reprocessing spent nuclear fuel. The ability to tune bonding and the coordination environment in these trivalent systems is a key factor in identifying a solution for separating lanthanides and actinides. Coordination of 4,4′−bipyridine (4,4′−bpy) and trimethylsilylcyclopentadienide (Cp′) to americium introduces unexpectedly ionic Am−N bonding character and unique spectroscopic properties. Here we report the structural characterization of (Cp′
3
Am)
2
(
μ
− 4,4′−bpy) and its lanthanide analogue, (Cp′
3
Nd)
2
(
μ
− 4,4′−bpy), by single-crystal X-ray diffraction. Spectroscopic techniques in both solid and solution phase are performed in conjunction with theoretical calculations to probe the effects the unique coordination environment has on the electronic structure.
The coordination environment has a great impact on the electronic structure, bonding and properties of metal complexes. Here the authors report a dinuclear organometallic americium complex that displays unexpectedly ionic Am−N bonding, but enhanced covalency in the Am−C bonds compared to its neodymium analogue.
Journal Article
Target cell-specific synaptic dynamics of excitatory to inhibitory neuron connections in supragranular layers of human neocortex
Rodent studies have demonstrated that synaptic dynamics from excitatory to inhibitory neuron types are often dependent on the target cell type. However, these target cell-specific properties have not been well investigated in human cortex, where there are major technical challenges in reliably obtaining healthy tissue, conducting multiple patch-clamp recordings on inhibitory cell types, and identifying those cell types. Here, we take advantage of newly developed methods for human neurosurgical tissue analysis with multiple patch-clamp recordings, post-hoc fluorescent in situ hybridization (FISH), machine learning-based cell type classification and prospective GABAergic AAV-based labeling to investigate synaptic properties between pyramidal neurons and PVALB- vs. SST-positive interneurons. We find that there are robust molecular differences in synapse-associated genes between these neuron types, and that individual presynaptic pyramidal neurons evoke postsynaptic responses with heterogeneous synaptic dynamics in different postsynaptic cell types. Using molecular identification with FISH and classifiers based on transcriptomically identified PVALB neurons analyzed by Patch-seq, we find that PVALB neurons typically show depressing synaptic characteristics, whereas other interneuron types including SST-positive neurons show facilitating characteristics. Together, these data support the existence of target cell-specific synaptic properties in human cortex that are similar to rodent, thereby indicating evolutionary conservation of local circuit connectivity motifs from excitatory to inhibitory neurons and their synaptic dynamics.
Journal Article
Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain
With the advent of multiplex fluorescence in situ hybridization (FISH) and in situ RNA sequencing technologies, spatial transcriptomics analysis is advancing rapidly, providing spatial location and gene expression information about cells in tissue sections at single cell resolution. Cell type classification of these spatially-resolved cells can be inferred by matching the spatial transcriptomics data to reference atlases derived from single cell RNA-sequencing (scRNA-seq) in which cell types are defined by differences in their gene expression profiles. However, robust cell type matching of the spatially-resolved cells to reference scRNA-seq atlases is challenging due to the intrinsic differences in resolution between the spatial and scRNA-seq data. In this study, we systematically evaluated six computational algorithms for cell type matching across four image-based spatial transcriptomics experimental protocols (MERFISH, smFISH, BaristaSeq, and ExSeq) conducted on the same mouse primary visual cortex (VISp) brain region. We find that many cells are assigned as the same type by multiple cell type matching algorithms and are present in spatial patterns previously reported from scRNA-seq studies in VISp. Furthermore, by combining the results of individual matching strategies into consensus cell type assignments, we see even greater alignment with biological expectations. We present two ensemble meta-analysis strategies used in this study and share the consensus cell type matching results in the Cytosplore Viewer (
https://viewer.cytosplore.org
) for interactive visualization and data exploration. The consensus matching can also guide spatial data analysis using SSAM, allowing segmentation-free cell type assignment.
Journal Article