Extensive GJD2 Expression in the Song Motor Pathway Reveals the Extent of Electrical Synapses in the Songbird Brain

Birdsong is a precisely timed animal behavior. The connectivity of song premotor neural networks has been proposed to underlie the temporal patterns of neuronal activity that control vo-cal muscle movements during singing. Although the connectivity of premotor nuclei via chemical synapses has been characterized, electrical synapses and their molecular identity remain unex-plored. We show with in situ hybridizations that GJD2 mRNA, coding for the major channel-form-ing electrical synapse protein in mammals, connexin 36, is expressed in the two nuclei that control song production, HVC and RA from canaries and zebra finches. In canaries’ HVC, GJD2 mRNA is extensively expressed in GABAergic and only a fraction of glutamatergic cells. By contrast, in RA, GJD2 mRNA expression is widespread in glutamatergic and GABAergic neurons. Remarkably, GJD2 expression is similar in song nuclei and their respective embedding brain regions, revealing the widespread expression of GJD2 in the avian brain. Inspection of a single-cell sequencing data-base from zebra and Bengalese finches generalizes the distributions of electrical synapses across cell types and song nuclei that we found in HVC and RA from canaries, reveals a differential GJD2 mRNA expression in HVC glutamatergic subtypes and its transient increase along the neurogenic lineage. We propose that songbirds are a suitable model to investigate the contribution of electrical synapses to motor skill learning and production.

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Asymmetry of an intracellular scaffold at vertebrate electrical synapses

10.1101/173955 ◽

2017 ◽

Author(s):

Audrey J Marsh ◽

Jennifer Carlisle Michel ◽

Anisha P Adke ◽

Emily L Heckman ◽

Adam C Miller

Keyword(s):

Gap Junction ◽

Synapse Formation ◽

Neural Circuit ◽

Electrical Synapse ◽

Electrical Synapses ◽

Gap Junction Channels ◽

Junction Protein ◽

Chemical Synapses ◽

And Function

AbstractNeuronal synaptic connections are electrical or chemical and together are essential to dynamically defining neural circuit function. While chemical synapses are well known for their biochemical complexity, electrical synapses are often viewed as comprised solely of neuronal gap junction channels that allow direct ionic and metabolic communication. However, associated with the gap junction channels are structures observed by electron microscopy called the Electrical Synapse Density (ESD). The ESD has been suggested to be critical for the formation and function of the electrical synapse, yet the biochemical makeup of these structures is poorly understood. Here we find that electrical synapse formation in vivo requires an intracellular scaffold called Tight Junction Protein 1b (Tjp1b). Tjp1b is localized to electrical synapses where it is required for the stabilization of the gap junction channels and for electrical synapse function. Strikingly, we find that Tjp1b protein localizes and functions asymmetrically, exclusively on the postsynaptic side of the synapse. Our findings support a novel model in which there is molecular asymmetry at the level of the intracellular scaffold that is required for building the electrical synapse. ESD molecular asymmetries may be a fundamental motif of all nervous systems and could support functional asymmetry at the electrical synapse.

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Electrical synaptic transmission in developing zebrafish: properties and molecular composition of gap junctions at a central auditory synapse

Journal of Neurophysiology ◽

10.1152/jn.00397.2014 ◽

2014 ◽

Vol 112 (9) ◽

pp. 2102-2113 ◽

Cited By ~ 19

Author(s):

Cong Yao ◽

Kimberly G. Vanderpool ◽

Matthew Delfiner ◽

Vanessa Eddy ◽

Alexander G. Lucaci ◽

...

Keyword(s):

Synaptic Transmission ◽

Gap Junctions ◽

Developmental Stages ◽

Neural Function ◽

Electrical Transmission ◽

Electrical Synapses ◽

Connexin 36 ◽

Auditory Responses ◽

Electrophysiological Recordings ◽

Chemical Synapses

In contrast to the knowledge of chemical synapses, little is known regarding the properties of gap junction-mediated electrical synapses in developing zebrafish, which provide a valuable model to study neural function at the systems level. Identifiable “mixed” (electrical and chemical) auditory synaptic contacts known as “club endings” on Mauthner cells (2 large reticulospinal neurons involved in tail-flip escape responses) allow exploration of electrical transmission in fish. Here, we show that paralleling the development of auditory responses, electrical synapses at these contacts become anatomically identifiable at day 3 postfertilization, reaching a number of ∼6 between days 4 and 9. Furthermore, each terminal contains ∼18 gap junctions, representing between 2,000 and 3,000 connexon channels formed by the teleost homologs of mammalian connexin 36. Electrophysiological recordings revealed that gap junctions at each of these contacts are functional and that synaptic transmission has properties that are comparable with those of adult fish. Thus a surprisingly small number of mixed synapses are responsible for the acquisition of auditory responses by the Mauthner cells, and these are likely sufficient to support escape behaviors at early developmental stages.

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FR-Match: Robust matching of cell type clusters from single cell RNA sequencing data using the Friedman-Rafsky non-parametric test

10.1101/2020.05.01.073445 ◽

2020 ◽

Author(s):

Yun Zhang ◽

Brian D. Aevermann ◽

Trygve E. Bakken ◽

Jeremy A. Miller ◽

Rebecca D. Hodge ◽

...

Keyword(s):

Human Brain ◽

Single Cell ◽

Rna Sequencing ◽

Cell Types ◽

R Package ◽

Brain Regions ◽

Cortical Layer ◽

Middle Temporal Gyrus ◽

Cell Type ◽

Sequencing Data

AbstractSingle cell/nucleus RNA sequencing (scRNAseq) is emerging as an essential tool to unravel the phenotypic heterogeneity of cells in complex biological systems. While computational methods for scRNAseq cell type clustering have advanced, the ability to integrate datasets to identify common and novel cell types across experiments remains a challenge. Here, we introduce a cluster-to-cluster cell type matching method – FR-Match – that utilizes supervised feature selection for dimensionality reduction and incorporates shared information among cells to determine whether two cell type clusters share the same underlying multivariate gene expression distribution. FR-Match is benchmarked with existing cell-to-cell and cell-to-cluster cell type matching methods using both simulated and real scRNAseq data. FR-Match proved to be a stringent method that produced fewer erroneous matches of distinct cell subtypes and had the unique ability to identify novel cell phenotypes in new datasets. In silico validation demonstrated that the proposed workflow is the only self-contained algorithm that was robust to increasing numbers of true negatives (i.e. non-represented cell types). FR-Match was applied to two human brain scRNAseq datasets sampled from cortical layer 1 and full thickness middle temporal gyrus. When mapping cell types identified in specimens isolated from these overlapping human brain regions, FR-Match precisely recapitulated the laminar characteristics of matched cell type clusters, reflecting their distinct neuroanatomical distributions. An R package and Shiny application are provided at https://github.com/JCVenterInstitute/FRmatch for users to interactively explore and match scRNAseq cell type clusters with complementary visualization tools.

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Cellular and genetic drivers of RNA editing variation in the human brain

10.1101/2021.07.16.452690 ◽

2021 ◽

Author(s):

Ryn Cuddleston ◽

Junhao Li ◽

Xuanjia Fan ◽

Alexey Kozenkov ◽

Matthew Lalli ◽

...

Keyword(s):

Human Brain ◽

Rna Sequencing ◽

Rna Editing ◽

Genetic Regulation ◽

Cell Types ◽

Brain Regions ◽

Brain Cell ◽

Cell Type ◽

Sequencing Data ◽

Regulatory Effects

Posttranscriptional adenosine-to-inosine modifications amplify the functionality of RNA molecules in the brain, yet the cellular and genetic regulation of RNA editing is poorly described. We quantified base-specific RNA editing across three major cell populations from the human prefrontal cortex: glutamatergic neurons, medial ganglionic eminence GABAergic neurons, and oligodendrocytes. We found more selective editing and RNA hyper-editing in neurons relative to oligodendrocytes. The pattern of RNA editing was highly cell type-specific, with 189,229 cell type-associated sites. The cellular specificity for thousands of sites was confirmed by single nucleus RNA-sequencing. Importantly, cell type-associated sites were enriched in GTEx RNA-sequencing data, edited ~twentyfold higher than all other sites, and variation in RNA editing was predominantly explained by neuronal proportions in bulk brain tissue. Finally, we discovered 661,791 cis-editing quantitative trait loci across thirteen brain regions, including hundreds with cell type-associated features. These data reveal an expansive repertoire of highly regulated RNA editing sites across human brain cell types and provide a resolved atlas linking cell types to editing variation and genetic regulatory effects.

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Synchronization of the neurons coupled with sequential developing electrical and chemical synapses

Mathematical Biosciences and Engineering ◽

10.3934/mbe.2022088 ◽

2021 ◽

Vol 19 (2) ◽

pp. 1877-1890

Author(s):

Zhen Wang ◽

◽

Ramesh Ramamoorthy ◽

Xiaojian Xi ◽

Hamidreza Namazi ◽

...

Keyword(s):

Mathematical Modeling ◽

Transition Period ◽

Brain Regions ◽

Synchronization Error ◽

Electrical Synapses ◽

Burst Synchronization ◽

Chemical Synapses ◽

Over Time ◽

Sequential Formation ◽

Modeling Study

<abstract> <p>There is some evidence representing the sequential formation and elimination of electrical and chemical synapses in particular brain regions. Relying on this feature, this paper presents a purely mathematical modeling study on the synchronization among neurons connected by transient electrical synapses transformed to chemical synapses over time. This deletion and development of synapses are considered consecutive. The results represent that the transient synapses lead to burst synchronization of the neurons while the neurons are resting when both synapses exist constantly. The period of the transitions and also the time of presence of electrical synapses to chemical ones are effective on the synchronization. The larger synchronization error is obtained by increasing the transition period and the time of chemical synapses' existence.</p> </abstract>

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FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman–Rafsky non-parametric test

Briefings in Bioinformatics ◽

10.1093/bib/bbaa339 ◽

2020 ◽

Author(s):

Yun Zhang ◽

Brian D Aevermann ◽

Trygve E Bakken ◽

Jeremy A Miller ◽

Rebecca D Hodge ◽

...

Keyword(s):

Human Brain ◽

Single Cell ◽

Rna Sequencing ◽

Cell Types ◽

R Package ◽

Brain Regions ◽

Cortical Layer ◽

Middle Temporal Gyrus ◽

Cell Type ◽

Sequencing Data

Abstract Single cell/nucleus RNA sequencing (scRNAseq) is emerging as an essential tool to unravel the phenotypic heterogeneity of cells in complex biological systems. While computational methods for scRNAseq cell type clustering have advanced, the ability to integrate datasets to identify common and novel cell types across experiments remains a challenge. Here, we introduce a cluster-to-cluster cell type matching method—FR-Match—that utilizes supervised feature selection for dimensionality reduction and incorporates shared information among cells to determine whether two cell type clusters share the same underlying multivariate gene expression distribution. FR-Match is benchmarked with existing cell-to-cell and cell-to-cluster cell type matching methods using both simulated and real scRNAseq data. FR-Match proved to be a stringent method that produced fewer erroneous matches of distinct cell subtypes and had the unique ability to identify novel cell phenotypes in new datasets. In silico validation demonstrated that the proposed workflow is the only self-contained algorithm that was robust to increasing numbers of true negatives (i.e. non-represented cell types). FR-Match was applied to two human brain scRNAseq datasets sampled from cortical layer 1 and full thickness middle temporal gyrus. When mapping cell types identified in specimens isolated from these overlapping human brain regions, FR-Match precisely recapitulated the laminar characteristics of matched cell type clusters, reflecting their distinct neuroanatomical distributions. An R package and Shiny application are provided at https://github.com/JCVenterInstitute/FRmatch for users to interactively explore and match scRNAseq cell type clusters with complementary visualization tools.

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Interactions of the Giant Fibres and Motor Giant Neurones of the Hermit Crab

Journal of Experimental Biology ◽

10.1242/jeb.133.1.353 ◽

1987 ◽

Vol 133 (1) ◽

pp. 353-370

Author(s):

W. J. HEITLER ◽

K. FRASER

Keyword(s):

Hermit Crab ◽

Electrical Synapse ◽

Chemical Synapse ◽

Electrical Synapses ◽

Giant Fibre ◽

Giant Neurone ◽

Giant Fibres ◽

Chemical Synapses ◽

Contralateral Motor ◽

Recent Claim

A recent claim that the giant fibre of the hermit crab excites its contralateral motor giant neurone through a chemical rather than an electrical synapse (Stephens, 1986) was re-examined. We found that the reported increased latency (relative to the electrical ipsilateral synapse) was postsynaptic in origin, as was the increased spike ‘jitter’. There was no difference in synaptic latency between the electrical synapse and the supposed chemical one. We did not find a consistent resistance to N-ethylmaleimide (an uncoupler of electrical synapses) by the supposed chemical synapse, but the synapse was resistant to 2 mmol 1−1 cadmium, which blocks known chemical synapses in the system. Sub-threshold depolarizing current passed from the presynaptic giant fibre to the postsynaptic contralateral motor giant, and hyperpolarizing current passed antidromically. We conclude that the synapse is electrical and not chemical in nature.

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Synaptic organization of the gustatory NST

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100168487 ◽

1994 ◽

Vol 52 ◽

pp. 150-151

Author(s):

M. C. Whitehead

Keyword(s):

Central Nervous System ◽

Dendritic Spines ◽

Fundamental Problem ◽

Cell Types ◽

Brain Regions ◽

Excitatory Synapses ◽

Solitary Tract ◽

Synaptic Organization ◽

Synaptic Junctions ◽

Afferent Terminals

A fundamental problem in taste research is to determine how gustatory signals are processed and disseminated in the mammalian central nervous system. An important first step toward understanding information processing is the identification of cell types in the nucleus of the solitary tract (NST) and their synaptic relationships with oral primary afferent terminals. Facial and glossopharyngeal (LIX) terminals in the hamster were labelled with HRP, examined with EM, and characterized as containing moderate concentrations of medium-sized round vesicles, and engaging in asymmetrical synaptic junctions. Ultrastructurally the endings resemble excitatory synapses in other brain regions.Labelled facial afferent endings in the RC subdivision synapse almost exclusively with distal dendrites and dendritic spines of NST cells. Most synaptic relationships between the facial synapses and the dendrites are simple. However, 40% of facial endings engage in complex synaptic relationships within glomeruli containing unlabelled axon endings particularly ones termed "SP" endings. SP endings are densely packed with small, pleomorphic vesicles and synapse with both the facial endings and their postsynaptic dendrites by means of nearly symmetrical junctions.

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In-depth transcriptomic analysis of human retina reveals molecular mechanisms underlying diabetic retinopathy

Scientific Reports ◽

10.1038/s41598-021-88698-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kolja Becker ◽

Holger Klein ◽

Eric Simon ◽

Coralie Viollet ◽

Christian Haslinger ◽

...

Keyword(s):

Diabetic Retinopathy ◽

Rna Sequencing ◽

Molecular Mechanisms ◽

Vision Loss ◽

Ganglion Cells ◽

Expression Profiles ◽

Cell Types ◽

Sequencing Data ◽

Disease Stages ◽

Post Transcriptional Regulation

AbstractDiabetic Retinopathy (DR) is among the major global causes for vision loss. With the rise in diabetes prevalence, an increase in DR incidence is expected. Current understanding of both the molecular etiology and pathways involved in the initiation and progression of DR is limited. Via RNA-Sequencing, we analyzed mRNA and miRNA expression profiles of 80 human post-mortem retinal samples from 43 patients diagnosed with various stages of DR. We found differentially expressed transcripts to be predominantly associated with late stage DR and pathways such as hippo and gap junction signaling. A multivariate regression model identified transcripts with progressive changes throughout disease stages, which in turn displayed significant overlap with sphingolipid and cGMP–PKG signaling. Combined analysis of miRNA and mRNA expression further uncovered disease-relevant miRNA/mRNA associations as potential mechanisms of post-transcriptional regulation. Finally, integrating human retinal single cell RNA-Sequencing data revealed a continuous loss of retinal ganglion cells, and Müller cell mediated changes in histidine and β-alanine signaling. While previously considered primarily a vascular disease, attention in DR has shifted to additional mechanisms and cell-types. Our findings offer an unprecedented and unbiased insight into molecular pathways and cell-specific changes in the development of DR, and provide potential avenues for future therapeutic intervention.

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scSorter: assigning cells to known cell types according to marker genes

Genome Biology ◽

10.1186/s13059-021-02281-7 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Hongyu Guo ◽

Jun Li

Keyword(s):

Real Data ◽

Cell Types ◽

Exact Expression ◽

Marker Genes ◽

Specific Marker ◽

Sequencing Data ◽

Reference Dataset ◽

Over Expression ◽

Higher Power ◽

Cell Type Specific

AbstractOn single-cell RNA-sequencing data, we consider the problem of assigning cells to known cell types, assuming that the identities of cell-type-specific marker genes are given but their exact expression levels are unavailable, that is, without using a reference dataset. Based on an observation that the expected over-expression of marker genes is often absent in a nonnegligible proportion of cells, we develop a method called scSorter. scSorter allows marker genes to express at a low level and borrows information from the expression of non-marker genes. On both simulated and real data, scSorter shows much higher power compared to existing methods.

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