scholarly journals A genetic, genomic, and computational resource for exploring neural circuit function

2018 ◽  
Author(s):  
Fred P. Davis ◽  
Aljoscha Nern ◽  
Serge Picard ◽  
Michael B. Reiser ◽  
Gerald M. Rubin ◽  
...  
Keyword(s):  
Neural Circuit ◽  
Affinity Purification ◽  
Probabilistic Method ◽  
Expression Patterns ◽  
Cell Types ◽  
Receptor Expression ◽  
List Type ◽  
Visual Neurons ◽  
Circuit Function ◽  
Different Cell Types

AbstractThe anatomy of many neural circuits is being characterized with increasing resolution, but their molecular properties remain mostly unknown. Here, we characterize gene expression patterns in distinct neural cell types of the Drosophila visual system using genetic lines to access individual cell types, the TAPIN-seq method to measure their transcriptomes, and a probabilistic method to interpret these measurements. We used these tools to build a resource of high-resolution transcriptomes for 100 driver lines covering 67 cell types, available at http://www.opticlobe.com. Combining these transcriptomes with recently reported connectomes helps characterize how information is transmitted and processed across a range of scales, from individual synapses to circuit pathways. We describe examples that include identifying neurotransmitters, including cases of co-release, generating functional hypotheses based on receptor expression, as well as identifying strong commonalities between different cell types.HighlightsTranscriptomes reveal transmitters and receptors expressed in Drosophila visual neuronsTandem affinity purification of intact nuclei (TAPIN) enables neuronal genomicsTAPIN-seq and genetic drivers establish transcriptomes of 67 Drosophila cell typesProbabilistic modeling simplifies interpretation of large transcriptome catalogs

scholarly journals A genetic, genomic, and computational resource for exploring neural circuit function

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Fred P Davis ◽  
Aljoscha Nern ◽  
Serge Picard ◽  
Michael B Reiser ◽  
Gerald M Rubin ◽  
...  
Keyword(s):  
Neural Circuits ◽  
Neural Circuit ◽  
Individual Cell ◽  
Probabilistic Method ◽  
Expression Patterns ◽  
Cell Types ◽  
Receptor Expression ◽  
Generating Functional ◽  
Circuit Function ◽  
Different Cell Types

The anatomy of many neural circuits is being characterized with increasing resolution, but their molecular properties remain mostly unknown. Here, we characterize gene expression patterns in distinct neural cell types of the Drosophila visual system using genetic lines to access individual cell types, the TAPIN-seq method to measure their transcriptomes, and a probabilistic method to interpret these measurements. We used these tools to build a resource of high-resolution transcriptomes for 100 driver lines covering 67 cell types, available at http://www.opticlobe.com. Combining these transcriptomes with recently reported connectomes helps characterize how information is transmitted and processed across a range of scales, from individual synapses to circuit pathways. We describe examples that include identifying neurotransmitters, including cases of apparent co-release, generating functional hypotheses based on receptor expression, as well as identifying strong commonalities between different cell types.

scholarly journals Chemical and Light Inducible Epigenome Editing

2020 ◽  
Vol 21 (3) ◽  
pp. 998
Author(s):  
Weiye Zhao ◽  
Yufan Wang ◽  
Fu-Sen Liang
Keyword(s):  
Small Molecules ◽  
Expression Patterns ◽  
Cell Types ◽  
Epigenome Editing ◽  
Specific Targeting ◽  
Conditional Control ◽  
Cellular Behaviors ◽  
Different Cell Types ◽  
Kinetics Of ◽  
Epigenetic Research

The epigenome defines the unique gene expression patterns and resulting cellular behaviors in different cell types. Epigenome dysregulation has been directly linked to various human diseases. Epigenome editing enabling genome locus-specific targeting of epigenome modifiers to directly alter specific local epigenome modifications offers a revolutionary tool for mechanistic studies in epigenome regulation as well as the development of novel epigenome therapies. Inducible and reversible epigenome editing provides unique temporal control critical for understanding the dynamics and kinetics of epigenome regulation. This review summarizes the progress in the development of spatiotemporal-specific tools using small molecules or light as inducers to achieve the conditional control of epigenome editing and their applications in epigenetic research.

scholarly journals Cell Specific Dopamine Modulation of the Transient Potassium Current in the Pyloric Network by the Canonical D1 Receptor Signal Transduction Cascade

2010 ◽  
Vol 104 (2) ◽  
pp. 873-884 ◽  
Author(s):  
Hongmei Zhang ◽  
Edmund W. Rodgers ◽  
Wulf-Dieter C. Krenz ◽  
Merry C. Clark ◽  
Deborah J. Baro
Keyword(s):  
Potassium Current ◽  
Expression System ◽  
Expression Patterns ◽  
Motor Pattern ◽  
Cell Types ◽  
Receptor Expression ◽  
Intracellular Camp ◽  
Cell Type ◽  
Pyloric Network ◽  
Cell Type Specific

Dopamine (DA) modifies the motor pattern generated by the pyloric network in the stomatogastric ganglion (STG) of the spiny lobster, Panulirus interruptus , by directly acting on each of the circuit neurons. The 14 pyloric neurons fall into six cell types, and DA actions are cell type specific. The transient potassium current mediated by shal channels ( IA) is a common target of DA modulation in most cell types. DA shifts the voltage dependence of IA in opposing directions in pyloric dilator (PD) versus lateral pyloric (LP) neurons. The mechanism(s) underpinning cell-type specific DA modulation of IA is unknown. DA receptors (DARs) can be classified as type 1 (D1R) or type 2 (D2R). D1Rs and D2Rs are known to increase and decrease intracellular cAMP concentrations, respectively. We hypothesized that the opposing DA effects on PD and LP IA were due to differences in DAR expression patterns. In the present study, we found that LP expressed somatodendritic D1Rs that were concentrated near synapses but did not express D2Rs. Consistently, DA modulation of LP IA was mediated by a Gs-adenylyl cyclase-cAMP-protein kinase A pathway. Additionally, we defined antagonists for lobster D1Rs (flupenthixol) and D2Rs (metoclopramide) in a heterologous expression system and showed that DA modulation of LP IA was blocked by flupenthixol but not by metoclopramide. We previously showed that PD neurons express D2Rs, but not D1Rs, thus supporting the idea that cell specific effects of DA on IA are due to differences in receptor expression.

scholarly journals Tumor Rejection by Disturbing Tumor Stroma Cell Interactions

2001 ◽  
Vol 194 (11) ◽  
pp. 1549-1560 ◽  
Author(s):  
Sabrina Ibe ◽  
Zhihai Qin ◽  
Thomas Schüler ◽  
Susanne Preiss ◽  
Thomas Blankenstein
Keyword(s):  
T Cells ◽  
Tumor Stroma ◽  
Residual Tumor ◽  
Cell Types ◽  
Cell Interactions ◽  
Tumor Rejection ◽  
Receptor Expression ◽  
Stroma Cell ◽  
Ifn Γ ◽  
Different Cell Types

The stroma of solid tumors is a complex network of different cell types. We analyzed stroma cell interactions in two tumor models during cyclophosphamide (Cy)-induced tumor rejection. In growing tumors, tumor infiltrating macrophages (TIMs) produced interleukin (IL)-10. Beginning 6 h after Cy-treatment T cells in the tumor were inactivated and TIMs switched to interferon (IFN)-γ production. Both, IL-10 production before and IFN-γ production after Cy-treatment by TIMs required T cells. With the same kinetics as TIMs started to produce IFN-γ the tumor vasculature was destroyed which required IFN-γ receptor expression on host but not tumor cells. These events preceded hemorrhagic necrosis and residual tumor cell elimination by T cells. Together, T cells regulate the function of TIMs and tumor rejection can be induced by disturbing the stroma network.

scholarly journals Global Analysis of Cell Type-Specific Gene Expression

2003 ◽  
Vol 4 (2) ◽  
pp. 208-215 ◽  
Author(s):  
David W. Galbraith
Keyword(s):  
Gene Expression ◽  
Fluorescent Protein ◽  
Global Analysis ◽  
Expression Patterns ◽  
Three Dimensional ◽  
Global Gene Expression ◽  
Cell Types ◽  
Reasonable Assumption ◽  
Specific Gene ◽  
Different Cell Types

The tissues and organs of multicellular eukaryotes are frequently observed to comprise complex three-dimensional interspersions of different cell types. It is a reasonable assumption that different global patterns of gene expression are found within these different cell types. This review outlines general experimental strategies designed to characterize these global gene expression patterns, based on a combination of methods of transgenic fluorescent protein (FP) expression and targeting, of flow cytometry and sorting and of high-throughput gene expression analysis.

Localization of Angiotensin II Type 1 receptor gene expression in rodent and human kidneys

2021 ◽  
Author(s):  
Julia Schrankl ◽  
Michaela Fuchs ◽  
Katharina Broeker ◽  
Christoph Daniel ◽  
Armin Kurtz ◽  
...  
Keyword(s):  
Angiotensin Ii ◽  
Mesangial Cells ◽  
Vascular System ◽  
Receptor Gene ◽  
Cell Types ◽  
Receptor Expression ◽  
Ang Ii ◽  
Comprehensive Overview ◽  
Different Cell Types

The kidneys are an important target for angiotensin II (ANG II). In the adult kidneys the effects of ANG II are mediated mainly by ANG II type 1 (AT1) receptors. AT1 receptor expression has been reported for a variety of different cell types within the kidneys, suggesting a broad spectrum of actions for ANG II. Since there have been heterogeneous results in the literature regarding the intrarenal distribution of AT1 receptors, this study aimed to obtain a comprehensive overview about the localization of AT1 receptor expression in mouse, rat and human kidneys. Using the cell specific and high-resolution RNAscope technique, we performed colocalization studies with various cell markers to specifically discriminate between different segments of the tubular and vascular system. Overall we found a similar pattern of AT1 mRNA expression in mouse, rat and human kidneys. AT1 receptors were detected in mesangial cells and renin-producing cells. In addition, AT1 mRNA was found in interstitial cells of the cortex and outer medulla. In rodents, late afferent and early efferent arterioles expressed AT1 receptor mRNA, but larger vessels of the investigated species showed no AT1 expression. Tubular expression of AT1 mRNA was species-dependent with a strong expression in proximal tubules of mice while expression was undetectable in human tubular cells. These findings suggest that the (juxta)glomerular area and the tubulointerstitium are conserved expression sites for AT1 receptors across species and might present the main target sites for ANG II in adult human and rodent kidneys.

scholarly journals Biophysical Support for Functionally Distinct Cell Types in the Frontal Eye Field

2009 ◽  
Vol 101 (2) ◽  
pp. 912-916 ◽  
Author(s):  
Jeremiah Y. Cohen ◽  
Pierre Pouget ◽  
Richard P. Heitz ◽  
Geoffrey F. Woodman ◽  
Jeffrey D. Schall
Keyword(s):  
Action Potentials ◽  
Cell Types ◽  
Frontal Eye Field ◽  
Subcortical Structures ◽  
Brain Areas ◽  
Visual Neurons ◽  
Distinct Cell ◽  
Eye Field ◽  
And Function ◽  
Different Cell Types

Numerous studies have described different functional cell types in the frontal eye field (FEF), but the reliability of the distinction between these types has been uncertain. Studies in other brain areas have described specific differences in the width of action potentials recorded from different cell types. To substantiate the functionally defined cell types encountered in FEF, we measured the width of spikes of visual, movement, and visuomovement types of FEF neurons in macaque monkeys. We show that visuomovement neurons had the thinnest spikes, consistent with a role in local processing. Movement neurons had the widest spikes, consistent with their role in sending eye movement commands to subcortical structures such as the superior colliculus. Visual neurons had wider spikes than visuomovement neurons, consistent with their role in receiving projections from occipital and parietal cortex. These results show how structure and function of FEF can be linked to guide inferences about neuronal architecture.

scholarly journals Cellular diversity in the Drosophila midbrain revealed by single-cell transcriptomics

2017 ◽  
Author(s):  
Vincent Croset ◽  
Christoph D Treiber ◽  
Scott Waddell
Keyword(s):  
Single Cell ◽  
Neural Circuit ◽  
Cell Types ◽  
Brain Regions ◽  
Neurotransmitter Receptor ◽  
Neural Processes ◽  
Subunit Expression ◽  
Circuit Function ◽  
Fast Acting ◽  
The Brain

AbstractTo understand the brain, molecular details need to be overlaid onto neural wiring diagrams so that synaptic mode, neuromodulation and critical signaling operations can be considered. Single-cell transcriptomics provide a unique opportunity to collect this information. Here we present an initial analysis of thousands of individual cells from Drosophila midbrain, that were acquired using Drop-Seq. A number of approaches permitted the assignment of transcriptional profiles to several major brain regions and cell-types. Expression of biosynthetic enzymes and reuptake mechanisms allows all the neurons to be typed according to the neurotransmitter or neuromodulator that they produce and presumably release. Some neuropeptides are preferentially co-expressed in neurons using a particular fast-acting transmitter, or monoamine. Neuromodulatory and neurotransmitter receptor subunit expression illustrates the potential of these molecules in generating complexity in neural circuit function. This cell atlas dataset provides an important resource to link molecular operations to brain regions and complex neural processes.

scholarly journals Store-independent modulation of Ca2+ entry through Orai by Septin 7

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Bipan Kumar Deb ◽  
Trayambak Pathak ◽  
Gaiti Hasan
Keyword(s):  
Neural Circuit ◽  
Cell Types ◽  
Negative Regulator ◽  
Flight Duration ◽  
Multiple Cell ◽  
Circuit Function ◽  
Trisphosphate Receptor ◽  
Molecular Brake ◽  
Orai Channels

Abstract Orai channels are required for store-operated Ca2+ entry (SOCE) in multiple cell types. Septins are a class of GTP-binding proteins that function as diffusion barriers in cells. Here we show that Septin 7 acts as a ‘molecular brake’ on activation of Orai channels in Drosophila neurons. Lowering Septin 7 levels results in dOrai-mediated Ca2+ entry and higher cytosolic Ca2+ in resting neurons. This Ca2+ entry is independent of depletion of endoplasmic reticulum Ca2+ stores and Ca2+ release through the inositol-1,4,5-trisphosphate receptor. Importantly, store-independent Ca2+ entry through Orai compensates for reduced SOCE in the Drosophila flight circuit. Moreover, overexpression of Septin 7 reduces both SOCE and flight duration, supporting its role as a negative regulator of Orai channel function in vivo. Septin 7 levels in neurons can, therefore, alter neural circuit function by modulating Orai function and Ca2+ homeostasis.

scholarly journals Cellular diversity in the Drosophila midbrain revealed by single-cell transcriptomics

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Vincent Croset ◽  
Christoph D Treiber ◽  
Scott Waddell
Keyword(s):  
Single Cell ◽  
Neural Circuit ◽  
Cell Types ◽  
Brain Regions ◽  
Neurotransmitter Receptor ◽  
Neural Processes ◽  
Subunit Expression ◽  
Circuit Function ◽  
Fast Acting ◽  
The Brain

To understand the brain, molecular details need to be overlaid onto neural wiring diagrams so that synaptic mode, neuromodulation and critical signaling operations can be considered. Single-cell transcriptomics provide a unique opportunity to collect this information. Here we present an initial analysis of thousands of individual cells from Drosophila midbrain, that were acquired using Drop-Seq. A number of approaches permitted the assignment of transcriptional profiles to several major brain regions and cell-types. Expression of biosynthetic enzymes and reuptake mechanisms allows all the neurons to be typed according to the neurotransmitter or neuromodulator that they produce and presumably release. Some neuropeptides are preferentially co-expressed in neurons using a particular fast-acting transmitter, or monoamine. Neuromodulatory and neurotransmitter receptor subunit expression illustrates the potential of these molecules in generating complexity in neural circuit function. This cell atlas dataset provides an important resource to link molecular operations to brain regions and complex neural processes.

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