ACD can configure probes for the various manual and automated assays for INS for RNAscope Assay, or for Basescope Assay compatible for your species of interest.
Nature communications
2023 Apr 27
Yang, SH;Yang, E;Lee, J;Kim, JY;Yoo, H;Park, HS;Jung, JT;Lee, D;Chun, S;Jo, YS;Pyeon, GH;Park, JY;Lee, HW;Kim, H;
PMID: 37105975 | DOI: 10.1038/s41467-023-38180-7
Neuron
2022 Sep 23
Yao, Y;Barger, Z;Saffari Doost, M;Tso, CF;Darmohray, D;Silverman, D;Liu, D;Ma, C;Cetin, A;Yao, S;Zeng, H;Dan, Y;
PMID: 36170850 | DOI: 10.1016/j.neuron.2022.08.027
Neuron
2017 Jun 29
Xiao L, Priest MF, Nasenbeny J, Lu T, Kozorovitskiy Y.
PMID: 28669546 | DOI: 10.1016/j.neuron.2017.06.003
The release of dopamine (DA) regulates rewarding behavior and motor actions through striatum-targeting efferents from ventral tegmental area (VTA) and substantia nigra pars compacta (SNc). Here, we map and functionally characterize axonal projections from oxytocin neurons in the hypothalamic paraventricular nucleus to midbrain DA regions. Electrophysiological recordings of DA neurons reveal that both the application of oxytocin and optogenetic stimulation of oxytocinergic terminals suffice to increase DA neuron activity in the VTA but downregulate it in SNc. This biased modulation is mediated by oxytocin and vasopressin G-protein-coupled receptors. Oxytocin release directly activates DA neurons and indirectly inhibits them through local GABA neurons, but the relative magnitudes of the two mechanisms differ in VTA and SNc. Oxytocin-modulated DA neurons give rise to canonical striatal projections. Since hypothalamic oxytocinergic projections also target the striatum, oxytocin is poised to bias the balance of DA tone through multiple sites in vertebrate reward circuits.
Cell rep
2020 Feb 18
Salesse C, Charest J, Doucet-Beaupr� H, Castonguay AM, Labrecque S, De Koninck P, L�vesque M
PMID: 32075770 | DOI: 10.1016/j.celrep.2020.01.084
Nature communications
2023 Jan 23
Jung, M;Dourado, M;Maksymetz, J;Jacobson, A;Laufer, BI;Baca, M;Foreman, O;Hackos, DH;Riol-Blanco, L;Kaminker, JS;
PMID: 36690629 | DOI: 10.1038/s41467-023-36014-0
JNeurosci
2017 Oct 24
Shi Y, Stornetta RL, Stornetta DS, Onengut-Gumuscu S, Farber EA, Turner SD, Guyenet PG, Bayliss DA.
PMID: 29066557 | DOI: 10.1523/JNEUROSCI.2055-17.2017
The retrotrapezoid nucleus (RTN) consists, by definition, of Phox2b-expressing, glutamatergic, non-catecholaminergic, non-cholinergic neurons located in the parafacial region of the medulla oblongata. An unknown proportion of RTN neurons are central respiratory chemoreceptors and there is mounting evidence for biochemical diversity among these cells. Here, we used multiplexed in situ hybridization and single-cell RNA-Seq in male and female mice to provide a more comprehensive view of the phenotypic diversity of RTN neurons. We now demonstrate that the RTN of mice can be identified with a single and specific marker, Nmb mRNA. Most (∼75%) RTN neurons express low-to-moderate levels of Nmb and display chemoreceptor properties. Namely they are activated by hypercapnia, but not by hypoxia, and express proton sensors, Kcnk5 and Gpr4 These Nmb-low RTN neurons also express varying levels of transcripts for Gal, Penk and Adcyap1,and receptors for substance P, orexin, serotonin and ATP. A subset of RTN neurons (∼20-25%), typically larger than average, express very high levels of Nmb mRNA. These Nmb-high RTN neurons do not express Fos after hypercapnia, have low-to-undetectable levels of Kcnk5 or Gpr4 transcripts; they also express Adcyap1, but are essentially devoid of Penk and Gal transcripts. In male rats, Nmb is also a marker of the RTN but, unlike in mice, this gene is expressed by other types of nearby neurons located within the ventromedial medulla. In sum, Nmb is a selective marker of the RTN in rodents; Nmb-low neurons, the vast majority, are central respiratory chemoreceptors whereas Nmb-high neurons likely have other functions.SIGNIFICANCE STATEMENTCentral respiratory chemoreceptors regulate arterial PCO2 by adjusting lung ventilation. Such cells have recently been identified within the retrotrapezoid nucleus (RTN), a brainstem nucleus defined by genetic lineage and a cumbersome combination of markers. Using single-cell RNA-Seq and multiplexed in situ hybridization, we show here that a single marker, Neuromedin B mRNA (Nmb), identifies RTN neurons in rodents. We also suggest that >75% of these Nmb neurons are chemoreceptors because they are strongly activated by hypercapnia and express high levels of proton sensors (Kcnk5 and Gpr4). The other RTN neurons express very high levels of Nmb, but low levels of Kcnk5/Gpr4/pre-pro-galanin/pre-pro-enkephalin, and do not respond to hypercapnia. Their function is unknown.
Cell Rep.
2018 May 22
Yan Y, Peng C, Arvin MC, Jin XT, Kim VJ, Ramsey MD, Wang Y, Banala S, Wokosin DL, McIntosh JM, Lavis LD, Drenan RM.
PMID: 29791835 | DOI: 10.1016/j.celrep.2018.04.062
Ventral tegmental area (VTA) glutamate neurons are important components of reward circuitry, but whether they are subject to cholinergic modulation is unknown. To study this, we used molecular, physiological, and photostimulation techniques to examine nicotinic acetylcholine receptors (nAChRs) in VTA glutamate neurons. Cells in the medial VTA, where glutamate neurons are enriched, are responsive to acetylcholine (ACh) released from cholinergic axons. VTA VGLUT2+ neurons express mRNA and protein subunits known to comprise heteromeric nAChRs. Electrophysiology, coupled with two-photon microscopy and laser flash photolysis of photoactivatable nicotine, was used to demonstrate nAChR functional activity in the somatodendritic subcellular compartment of VTA VGLUT2+ neurons. Finally, optogenetic isolation of intrinsic VTA glutamatergic microcircuits along with gene-editing techniques demonstrated that nicotine potently modulates excitatory transmission within the VTA via heteromeric nAChRs. These results indicate that VTA glutamate neurons are modulated by cholinergic mechanisms and participate in the cascade of physiological responses to nicotine exposure.
Cell
2018 Aug 02
Shrestha BR, Chia C, Wu L, Kujawa SG, Liberman MC, Goodrich LV.
PMID: - | DOI: 10.1016/j.cell.2018.07.007
In the auditory system, type I spiral ganglion neurons (SGNs) convey complex acoustic information from inner hair cells (IHCs) to the brainstem. Although SGNs exhibit variation in physiological and anatomical properties, it is unclear which features are endogenous and which reflect input from synaptic partners. Using single-cell RNA sequencing, we derived a molecular classification of mouse type I SGNs comprising three subtypes that express unique combinations of Ca 2+ binding proteins, ion channel regulators, guidance molecules, and transcription factors. Based on connectivity and susceptibility to age-related loss, these subtypes correspond to those defined physiologically. Additional intrinsic differences among subtypes and across the tonotopic axis highlight an unexpectedly active role for SGNs in auditory processing. SGN identities emerge postnatally and are disrupted in a mouse model of deafness that lacks IHC-driven activity. These results elucidate the range, nature, and origins of SGN diversity, with implications for treatment of congenital deafness.
Cells
2021 Dec 10
Barr, JL;Kruse, A;Restaino, AC;Tulina, N;Stuckelberger, S;Vermeer, SJ;Williamson, CS;Vermeer, DW;Madeo, M;Stamp, J;Bell, M;Morgan, M;Yoon, JY;Mitchell, MA;Budina, A;Omran, DK;Schwartz, LE;Drapkin, R;Vermeer, PD;
PMID: 34944001 | DOI: 10.3390/cells10123491
eNeuro
2018 May 21
Kramer DJ, Risso D, Kosillo P, Ngai J, Bateup HS.
PMID: - | DOI: 10.1523/eneuro.0152-18.2018
Midbrain dopamine neurons project to numerous targets throughout the brain to modulate various behaviors and brain states. Within this small population of neurons exists significant heterogeneity based on physiology, circuitry, and disease susceptibility. Recent studies have shown that dopamine neurons can be subdivided based on gene expression; however, the extent to which genetic markers represent functionally relevant dopaminergic subpopulations has not been fully explored. Here we performed single-cell RNA-sequencing of mouse dopamine neurons and validated studies showing that Neurod6 and Grp are selective markers for dopaminergic subpopulations. Using a combination of multiplex fluorescent in situ hybridization, retrograde labeling, and electrophysiology in mice of both sexes, we defined the anatomy, projection targets, physiological properties, and disease vulnerability of dopamine neurons based on Grp and/or Neurod6 expression. We find that the combinatorial expression of Grp and Neurod6 defines dopaminergic subpopulations with unique features. Grp+/Neurod6+ dopamine neurons reside in the ventromedial VTA, send projections to the medial shell of the nucleus accumbens, and have non-canonical physiological properties. Grp+/Neurod6- DA neurons are found in the VTA as well as in the ventromedial portion of the SNc where they project selectively to the dorsomedial striatum. Grp-/Neurod6+ DA neurons represent a smaller VTA subpopulation, which is preferentially spared in a 6-OHDA model of Parkinson’s disease. Together our work provides detailed characterization of Neurod6 and Grp expression in the midbrain and generates new insights into how these markers define functionally relevant dopaminergic subpopulations with distinct projection patterns, physiology, and disease vulnerability.
Significance Statement Recent single cell gene profiling studies have uncovered new subpopulations of midbrain dopamine neurons defined by their specific genetic signature. How these genetically-defined cell types map onto known dopaminergic circuits and functionally-defined cell types is unknown. This study elucidates the anatomy, circuitry, physiologic properties, and disease susceptibility of subpopulations of midbrain DA neurons defined by their expression of two genetic markers. This work not only advances our understanding of the dopaminergic system by providing new information about the properties of specific dopamine neuron subpopulations, it also demonstrates that unbiased genetic classification of neurons can reveal functionally relevant cell types.
Front. Neurosci.
2019 Feb 19
Hernadez-Perez OR, Hernandez VS, Nava-Kopp A, Barrio RA, Seifi M, Swinny JD, Eiden LE, Zhang L.
PMID: - | DOI: 10.3389/fnins.2019.00196
The locus coeruleus (LC)-norepinephrine (NE) system modulates a range of salient brain functions, including memory and response to stress. The LC-NE system is regulated by neurochemically diverse inputs, including a range of neuropeptides such as arginine-vasopressin (AVP). Whilst the origins of many of these LC inputs, their synaptic connectivity with LC neurons, and their contribution to LC-mediated brain functions, have been well characterized, this is not the case for the AVP-LC system. Therefore, our aims were to define the types of synapses formed by AVP+ fibers with LC neurons using immunohistochemistry together with confocal and transmission electron microscopy (TEM), the origins of such inputs, using retrograde tracers, and the plasticity of the LC AVP system in response to stress and spatial learning, using the maternal separation (MS) and Morris water maze (MWM) paradigms respectively, in rat. Confocal microscopy revealed that AVP+ fibers contacting tyrosine hydroxylase (TH)+ LC neurons were also immunopositive for vesicular glutamate transporter 2, a marker of presynaptic glutamatergic axons. TEM confirmed that AVP+ axons formed Gray type I (asymmetric) synapses with TH+ dendrites thus confirming excitatory synaptic connections between these systems. Retrograde tracing revealed that these LC AVP+ fibers originate from hypothalamic vasopressinergic magnocellular neurosecretory neurons (AVPMN). MS induced a significant increase in the density of LC AVP+ fibers. Finally, AVPMNN circuit upregulation by water-deprivation improved MWM performance while increased Fos expression was found in LC and efferent regions such as hippocampus and prefrontal cortex, suggesting that AVPMMN projections to LC could integrate homeostatic responses modifying neuroplasticity.
The Journal of comparative neurology
2022 Feb 08
Karthik, S;Huang, D;Delgado, Y;Laing, JJ;Peltekian, L;Iverson, GN;Grady, F;Miller, RL;McCann, CM;Fritzsch, B;Iskusnykh, IY;Chizhikov, VV;Geerling, JC;
PMID: 35134251 | DOI: 10.1002/cne.25307
Description | ||
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sense Example: Hs-LAG3-sense | Standard probes for RNA detection are in antisense. Sense probe is reverse complent to the corresponding antisense probe. | |
Intron# Example: Mm-Htt-intron2 | Probe targets the indicated intron in the target gene, commonly used for pre-mRNA detection | |
Pool/Pan Example: Hs-CD3-pool (Hs-CD3D, Hs-CD3E, Hs-CD3G) | A mixture of multiple probe sets targeting multiple genes or transcripts | |
No-XSp Example: Hs-PDGFB-No-XMm | Does not cross detect with the species (Sp) | |
XSp Example: Rn-Pde9a-XMm | designed to cross detect with the species (Sp) | |
O# Example: Mm-Islr-O1 | Alternative design targeting different regions of the same transcript or isoforms | |
CDS Example: Hs-SLC31A-CDS | Probe targets the protein-coding sequence only | |
EnEm | Probe targets exons n and m | |
En-Em | Probe targets region from exon n to exon m | |
Retired Nomenclature | ||
tvn Example: Hs-LEPR-tv1 | Designed to target transcript variant n | |
ORF Example: Hs-ACVRL1-ORF | Probe targets open reading frame | |
UTR Example: Hs-HTT-UTR-C3 | Probe targets the untranslated region (non-protein-coding region) only | |
5UTR Example: Hs-GNRHR-5UTR | Probe targets the 5' untranslated region only | |
3UTR Example: Rn-Npy1r-3UTR | Probe targets the 3' untranslated region only | |
Pan Example: Pool | A mixture of multiple probe sets targeting multiple genes or transcripts |
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