Explore the vast range of titles available.

The striatum integrates excitatory inputs from the cortex and the thalamus to control diverse functions. Although the striatum is thought to consist of sensorimotor, associative and limbic domains, their precise demarcations and whether additional functional subdivisions exist remain unclear. How striatal inputs are differentially segregated into each domain is also poorly understood. This study presents a comprehensive map of the excitatory inputs to the mouse striatum. The input patterns reveal boundaries between the known striatal domains. The most posterior striatum likely represents the 4th functional subdivision, and the dorsomedial striatum integrates highly heterogeneous, multimodal inputs. The complete thalamo-cortico-striatal loop is also presented, which reveals that the thalamic subregions innervated by the basal ganglia preferentially interconnect with motor-related cortical areas. Optogenetic experiments show the subregion-specific heterogeneity in the synaptic properties of striatal inputs from both the cortex and the thalamus. This projectome will guide functional studies investigating diverse striatal functions. To fully understand how the brain works, we need to understand how different brain structures are organized and how information flows between these structures. For example, the cortex and thalamus communicate with another structure known as the basal ganglia, which is essential for controlling voluntary movement, emotions and reward behaviour in humans and other mammals. Information from the cortex and the thalamus enters the basal ganglia at an area called the striatum. This area is further divided into smaller functional regions known as domains that sort sensorimotor, emotion and executive information into the basal ganglia to control different types of behaviour. Three such domains have been identified in the striatum of mice. However, the boundaries between these domains are vague and it is not clear whether any other domains exist or if the domains can actually be divided into even smaller areas with more precise roles. Information entering the striatum from other parts of the brain can either stimulate activity in the striatum (known as an “excitatory input”) or alter existing excitatory inputs. Now, Hunnicutt et al. present the first comprehensive map of excitatory inputs into the striatum of mice. The experiments show that while many of the excitatory inputs flowing into the striatum from the cortex and thalamus are sorted into the three known domains, a unique combination of the excitatory inputs are sorted into a new domain instead. One of the original three domains of the striatum is known to relay information related to associative learning, for example, linking an emotion to a person or place. Hunnicutt et al. show that this domain has a more complex architecture than the other domains, being made up of many distinct areas. This complexity may help it to process the various types of information required to make such associations. The findings of Hunnicutt et al. provide a framework for understanding how the striatum works in healthy and diseased brains. Since faulty information processing in the striatum is a direct cause of Parkinson’s disease, Huntington’s disease and other neurological disorders in humans, this framework may aid the development of new treatments for these disorders.

Coded aperture X-ray computed tomography (CAXCT) measures coded X-ray projections to reconstruct the inner structure of an object. Coded apertures, which determine the point spread function, can be designed to improve the reconstruction quality, but most approaches are computationally expensive, leading to very small images. In this paper, a sparse covariance matrix estimation approach is introduced to minimize the information loss sensed by projections corresponding to large tomographic images. The covariance matrix representing the map of the overlapping information of the projections is obtained by using block matrix multiplication and sparse estimation. A heuristic variant algorithm with a noise factor is presented to search the combinations of projections leading to maximum non-overlapping information acquisition, where is the number of unblocking elements on the coded apertures. Numerical experiments with simulated datasets show that the optimization performance of the proposed method is comparable to that of state-of-the-art methods with small images. Further, for the analyzed cases, coded aperture optimization was performed with 512 × 512 images by analyzing coefficients smaller than 0.02% in the covariance matrix.

Cortical mapping: subcellular organization The mapping of neuronal connections in the cerebral cortex has traditionally relied on electrophysiological recordings performed on brain slices, in which long-range connections are severed. Karel Svoboda and colleagues have now adapted a recent optogenetic method to map long-range inputs onto various segments of the dendritic arbours of cortical pyramidal neurons. They find that specific inputs tend to cluster in distinct domains within dendritic trees. Such spatial segregation of different axonal inputs within dendrites may strengthen coupling of coherent cell populations during neuronal information processing and learning. A recent optogenetic method has been adapted to map long-range inputs onto various segments of the dendritic arborizations of cortical pyramidal neurons. Specific inputs tend to cluster in distinct domains within dendritic trees. Such spatial segregation of different axonal inputs within dendrites may strengthen coupling of coherent cell populations during neuronal information processing and learning. Understanding cortical circuits will require mapping the connections between specific populations of neurons 1 , as well as determining the dendritic locations where the synapses occur 2 . The dendrites of individual cortical neurons overlap with numerous types of local and long-range excitatory axons, but axodendritic overlap is not always a good predictor of actual connection strength 3 , 4 , 5 . Here we developed an efficient channelrhodopsin-2 (ChR2)-assisted method 6 , 7 , 8 to map the spatial distribution of synaptic inputs, defined by presynaptic ChR2 expression, within the dendritic arborizations of recorded neurons. We expressed ChR2 in two thalamic nuclei, the whisker motor cortex and local excitatory neurons and mapped their synapses with pyramidal neurons in layers 3, 5A and 5B (L3, L5A and L5B) in the mouse barrel cortex. Within the dendritic arborizations of L3 cells, individual inputs impinged onto distinct single domains. These domains were arrayed in an orderly, monotonic pattern along the apical axis: axons from more central origins targeted progressively higher regions of the apical dendrites. In L5 arborizations, different inputs targeted separate basal and apical domains. Input to L3 and L5 dendrites in L1 was related to whisker movement and position, suggesting that these signals have a role in controlling the gain of their target neurons 9 . Our experiments reveal high specificity in the subcellular organization of excitatory circuits.

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.

The canonical model of striatal function predicts that animal locomotion is associated with the opposing regulation of protein kinase A (PKA) in direct and indirect pathway striatal spiny projection neurons (SPNs) by dopamine 1 – 7 . However, the precise dynamics of PKA in dorsolateral SPNs during locomotion remain to be determined. It is also unclear whether other neuromodulators are involved. Here we show that PKA activity in both types of SPNs is essential for normal locomotion. Using two-photon fluorescence lifetime imaging 8 – 10 of a PKA sensor 10 through gradient index lenses, we measured PKA activity within individual SPNs of the mouse dorsolateral striatum during locomotion. Consistent with the canonical view, dopamine activated PKA activity in direct pathway SPNs during locomotion through the dopamine D 1  receptor. However, indirect pathway SPNs exhibited a greater increase in PKA activity, which was largely abolished through the blockade of adenosine A 2A  receptors. In agreement with these results, fibre photometry measurements of an adenosine sensor 11 revealed an acute increase in extracellular adenosine during locomotion. Functionally, antagonism of dopamine or adenosine receptors resulted in distinct changes in SPN PKA activity, neuronal activity and locomotion. Together, our results suggest that acute adenosine accumulation interplays with dopamine release to orchestrate PKA activity in SPNs and proper striatal function during animal locomotion. Dopamine and adenosine act together in the striatum to regulate protein kinase A activity, which in turn coordinates animal locomotion.

This study describes the generation of knock-in mouse lines that express optogenetic activators or silencers in a CRE recombinase–dependent manner, and demonstrates the reliability and utility of these tools with in vivo and ex vivo light-induced activation and silencing of neuronal activity. Cell type–specific expression of optogenetic molecules allows temporally precise manipulation of targeted neuronal activity. Here we present a toolbox of four knock-in mouse lines engineered for strong, Cre-dependent expression of channelrhodopsins ChR2-tdTomato and ChR2-EYFP, halorhodopsin eNpHR3.0 and archaerhodopsin Arch-ER2. All four transgenes mediated Cre-dependent, robust activation or silencing of cortical pyramidal neurons in vitro and in vivo upon light stimulation, with ChR2-EYFP and Arch-ER2 demonstrating light sensitivity approaching that of in utero or virally transduced neurons. We further show specific photoactivation of parvalbumin-positive interneurons in behaving ChR2-EYFP reporter mice. The robust, consistent and inducible nature of our ChR2 mice represents a significant advance over previous lines, and the Arch-ER2 and eNpHR3.0 mice are to our knowledge the first demonstration of successful conditional transgenic optogenetic silencing. When combined with the hundreds of available Cre driver lines, this optimized toolbox of reporter mice will enable widespread investigations of neural circuit function with unprecedented reliability and accuracy.

The medial thalamus (MThal), anterior cingulate cortex (ACC) and striatum play important roles in affective-motivational pain processing and reward learning. Opioids affect both pain and reward through uncharacterized modulation of this circuitry. This study examined opioid actions on glutamate transmission between these brain regions in mouse. Mu-opioid receptor (MOR) agonists potently inhibited MThal inputs without affecting ACC inputs to individual striatal medium spiny neurons (MSNs). MOR activation also inhibited MThal inputs to the pyramidal neurons in the ACC. In contrast, delta-opioid receptor (DOR) agonists disinhibited ACC pyramidal neuron responses to MThal inputs by suppressing local feed-forward GABA signaling from parvalbumin-positive interneurons. As a result, DOR activation in the ACC facilitated poly-synaptic (thalamo-cortico-striatal) excitation of MSNs by MThal inputs. These results suggest that opioid effects on pain and reward may be shaped by the relative selectivity of opioid drugs to the specific circuit components.

Neuromodulators impose powerful control over brain function via their regulation of intracellular signaling through G-protein coupled receptors. In contrast to those of Gs and Gi pathways, in vivo imaging of the signaling events downstream of Gq-coupled receptors remains challenging. Here, we introduce CKAR3, a genetically encoded fluorescence lifetime sensor that reports the activity of protein kinase C (PKC), a major downstream effector of the Gq pathway. CKAR3 exhibits a lifetime dynamic range 5-fold larger than any existing PKC sensor. It specifically detects PKC phosphorylation with seconds kinetics without perturbing neuronal functions. In vivo two-photon lifetime imaging of CKAR3 reveals tonic PKC activity in cortical neurons. Animal locomotion elicits robust PKC activity in sparse neuronal ensembles in the motor cortex. Both basal and locomotion-elicited PKC activities are in part mediated by muscarinic acetylcholine receptors. Overall, CKAR3 enables interrogation of Gq signaling dynamics mediated by PKC in behaving animals. Neuromodulators that activate Gq-coupled receptors exert powerful control over brain function. Here, the authors develop a fluorescence lifetime sensor capable of imaging protein kinase C activity—a major effector of the Gq pathway—at cellular resolution in vivo.

Precise and efficient insertion of large DNA fragments into somatic cells using gene editing technologies to label or modify endogenous proteins remains challenging. Non-specific insertions/deletions (INDELs) resulting from the non-homologous end joining pathway make the process error-prone. Further, the insert is not readily removable. Here, we describe a method called CRISP R-mediated i nsertion of e xon (CRISPIE) that can precisely and reversibly label endogenous proteins using CRISPR/Cas9-based editing. CRISPIE inserts a designer donor module, which consists of an exon encoding the protein sequence flanked by intron sequences, into an intronic location in the target gene. INDELs at the insertion junction will be spliced out, leaving mRNAs nearly error-free. We used CRISPIE to fluorescently label endogenous proteins in mammalian neurons in vivo with previously unachieved efficiency. We demonstrate that this method is broadly applicable, and that the insert can be readily removed later. CRISPIE permits protein sequence insertion with high fidelity, efficiency, and flexibility.

Light-sheet microscopy has made possible the 3D imaging of both fixed and live biological tissue, with samples as large as the entire mouse brain. However, segmentation and quantification of that data remains a time-consuming manual undertaking. Machine learning methods promise the possibility of automating this process. This study seeks to advance the performance of prior models through optimizing transfer learning. We fine-tuned the existing TrailMap model using expert-labeled data from noradrenergic axonal structures in the mouse brain. By changing the cross-entropy weights and using augmentation, we demonstrate a generally improved adjusted F1-score over using the originally trained TrailMap model within our test datasets.