scholarly journals Nuclear transcriptomes of the seven neuronal cell types that constitute the Drosophila mushroom bodies

2018 ◽  
Author(s):  
Meng-Fu Maxwell Shih ◽  
Fred P. Davis ◽  
Gilbert Lee Henry ◽  
Josh Dubnau
Keyword(s):  
Neuronal Cell ◽  
Cell Types ◽  
Mushroom Bodies ◽  
Rna Seq ◽  
Memory Processing ◽  
Neuropeptide Receptors ◽  
Invertebrate Model ◽  
And Function ◽  
And Storage ◽  
Neuroscience Community

ABSTRACTThe insect mushroom body (MB) is a conserved brain structure that plays key roles in a diverse array of behaviors. The Drosophila melanogaster MB is the primary invertebrate model of neural circuits related to memory formation and storage, and its development, morphology, wiring, and function has been extensively studied. MBs consist of intrinsic Kenyon Cells that are divided into three major neuron classes (γ, α’/β’ and α/β) and 7 cell subtypes (γd, γm, α’/β’ap, α’/β’m, α/βp, α/βs and α/βc) based on their birth order, morphology, and connectivity. These subtypes play distinct roles in memory processing, however the underlying transcriptional differences are unknown. Here, we used RNA sequencing (RNA-seq) to profile the nuclear transcriptomes of each MB neuronal cell subtypes. We identified 350 MB class- or subtype-specific genes, including the widely used α/β class marker Fas2 and the α’/β’ class marker trio. Immunostaining corroborates the RNA-seq measurements at the protein level for several cases. Importantly, our data provide a full accounting of the neurotransmitter receptors, transporters, neurotransmitter biosynthetic enzymes, neuropeptides, and neuropeptide receptors expressed within each of these cell types. This high-quality, cell type-level transcriptome catalog for the Drosophila MB provides a valuable resource for the fly neuroscience community.

Form and Function in Cells of the Brain

The Neuron ◽  
2015 ◽  
pp. 23-38
Author(s):  
Irwin B. Levitan ◽  
Leonard K. Kaczmarek
Keyword(s):  
Axonal Transport ◽  
Molecular Motors ◽  
Critical Role ◽  
Neuronal Cell ◽  
Cell Types ◽  
Neuronal Cell Body ◽  
Long Distance ◽  
Form And Function ◽  
And Function ◽  
The Brain

This chapter examines unique mechanisms that the neuron has evolved to establish and maintain the form required for its specialized signaling functions. Unlike some other organs, the brain contains a variety of cell types including several classes of glial cells, which play a critical role in the formation of the myelin sheath around axons and may be involved in immune responses, synaptic transmission, and long-distance calcium signaling in the brain. Neurons share many features in common with other cells (including glia), but they are distinguished by their highly asymmetrical shapes. The neuronal cytoskeleton is essential for establishing this cell shape during development and for maintaining it in adulthood. The process of axonal transport moves vesicles and other organelles to regions remote from the neuronal cell body. Proteins such as kinesin and dynein, called molecular motors, make use of the energy released by hydrolysis of ATP to drive axonal transport.

scholarly journals A cellular and spatial map of the choroid plexus across brain ventricles and ages

2019 ◽  
Author(s):  
Neil Dani ◽  
Rebecca H. Herbst ◽  
Naomi Habib ◽  
Joshua Head ◽  
Danielle Dionne ◽  
...  
Keyword(s):  
Choroid Plexus ◽  
Adult Mouse ◽  
Cell Types ◽  
Rna Seq ◽  
Adult Mouse Brain ◽  
Brain Ventricles ◽  
Future Studies ◽  
Brain Ventricle ◽  
Macrophage Populations ◽  
And Function

AbstractThe choroid plexus (ChP), located in each brain ventricle, produces cerebrospinal fluid (CSF) and forms the blood-CSF barrier, but is under-characterized. Here, we combine single cell RNA-Seq and spatial mapping of RNA and proteins to construct an atlas of each ChP in the developing and adult mouse brain. Each ChP comprises of epithelial, endothelial, mesenchymal, immune, neuronal, and glial cells, with distinct subtypes, differentiation states and anatomical locations. Epithelial, fibroblast, and macrophage populations had ventricle-specific, regionalized gene expression programs across the developing brain. Key cell types are retained in adult, with loss of developmental signatures and maturation of ventricle-specific regionalization in the epithelial cells. Expression of cognate ligand-receptor pairs across cell subtypes suggests substantial cell-cell interactions within the ChP. Our atlas sheds new light on the development and function of the ChP brain barrier system, and will facilitate future studies on its role in brain development, homeostasis and disease.

scholarly journals MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data

2020 ◽  
Vol 21 (5) ◽  
pp. 1754 ◽  
Author(s):  
Enrico Gaffo ◽  
Michele Bortolomeazzi ◽  
Andrea Bisognin ◽  
Piero Di Battista ◽  
Federica Lovisa ◽  
...  
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Cell Types ◽  
Small Rna Sequencing ◽  
Rna Seq ◽  
Sequencing Data ◽  
Research Findings ◽  
Human Blood Cell ◽  
And Function ◽  
Comprehensive Study

MicroRNA-offset RNAs (moRNAs) are microRNA-like small RNAs generated by microRNA precursors. To date, little is known about moRNAs and bioinformatics tools to inspect their expression are still missing. We developed miR&moRe2, the first bioinformatics method to consistently characterize microRNAs, moRNAs, and their isoforms from small RNA sequencing data. To illustrate miR&moRe2 discovery power, we applied it to several published datasets. MoRNAs identified by miR&moRe2 were in agreement with previous research findings. Moreover, we observed that moRNAs and new microRNAs predicted by miR&moRe2 were downregulated upon the silencing of the microRNA-biogenesis pathway. Further, in a sizeable dataset of human blood cell populations, tens of novel miRNAs and moRNAs were discovered, some of them with significantly varied expression levels among the cell types. Results demonstrate that miR&moRe2 is a valid tool for a comprehensive study of small RNAs generated from microRNA precursors and could help to investigate their biogenesis and function.

Tuning the Elasticity of Biopolymer Gels for Optimal Wound Healing

2005 ◽  
Vol 897 ◽  
Author(s):  
Penelope Georges ◽  
Margaret McCormick ◽  
Lisa Flanagan ◽  
Yo-El Ju ◽  
Evelyn Sawyer ◽  
...  
Keyword(s):  
Cell Structure ◽  
Polymer Networks ◽  
Neuronal Cell ◽  
Mesh Size ◽  
Cell Types ◽  
Animal Cells ◽  
Normal Environment ◽  
Biopolymer Gels ◽  
Soft Polymer ◽  
And Function

AbstractSoft polymer networks with large mesh size, not flat rigid surfaces, are the normal environment for most animal cells. Cell structure and function depend on the stiffness of the surfaces on which cells adhere as well as on the type of adhesion complex by which the cell binds its extracellular ligand. Many cell types, including fibroblasts and endothelial cells, switch from a round to spread morphology as stiffness is increased between 1000 and 10,000 Pa. Coincident with the change in morphology are a host of differences in protein phosphorylation levels, expression of integrins, and changes in cytoskeletal protein expression and assembly. In contrast, other cells types such as neutrophils and platelets do not require rigid substrates in order to spread, and neurons extend processes better on soft (50 Pa) materials than on stiffer gels. We compare the stiffness sensing of four cell types: platelets, neurons and astrocytes, a glial cell type derived from embryonic rat brain, and melanoma cells. Astrocytes switch from a round to spread morphology as substrate stiffness increases, but do so over a stiffness range 10 times softer than that over which fibroblasts alter morphology. Stiffness-dependent morphologic changes observed from studies of cells grown on surfaces of protein-laminated polyacrylamide gels that have linear elasticity are also seen when cells are on matrices of natural biopolymers such as fibrin. Biopolymer gels like fibrin can be formed with appropriate stiffness to optimize for neuronal cell survival and patterning, and may have utility for repair of damaged neural tissues. The complex non-linear rheology of fibrin and other gels formed by semi-flexible biopolymers that exhibit strain-stiffening provide additional mechanisms by which cells can respond to and actively remodel the mechanical features of their environment.

scholarly journals Nuclear Transcriptomes of the Seven Neuronal Cell Types That Constitute the Drosophila Mushroom Bodies

2018 ◽  
Vol 9 (1) ◽  
pp. 81-94 ◽  
Author(s):  
Meng-Fu Maxwell Shih ◽  
Fred Pejman Davis ◽  
Gilbert Lee Henry ◽  
Josh Dubnau
Keyword(s):  
Neuronal Cell ◽  
Cell Types ◽  
Mushroom Bodies

scholarly journals Equivalent high-resolution identification of neuronal cell types with single-nucleus and single-cell RNA-sequencing

2017 ◽  
Author(s):  
Trygve E. Bakken ◽  
Rebecca D. Hodge ◽  
Jeremy M. Miller ◽  
Zizhen Yao ◽  
Thuc N. Nguyen ◽  
...  
Keyword(s):  
High Resolution ◽  
Single Cell ◽  
Rna Sequencing ◽  
Transcriptional Profiling ◽  
Neuronal Cell ◽  
Cell Types ◽  
Matched Pair ◽  
Rna Seq ◽  
Nuclear Rna ◽  
Single Nucleus

AbstractTranscriptional profiling of complex tissues by RNA-sequencing of single nuclei presents some advantages over whole cell analysis. It enables unbiased cellular coverage, lack of cell isolation-based transcriptional effects, and application to archived frozen specimens. Using a well-matched pair of single-nucleus RNA-seq (snRNA-seq) and single-cell RNA-seq (scRNA-seq) SMART-Seq v4 datasets from mouse visual cortex, we demonstrate that similarly high-resolution clustering of closely related neuronal types can be achieved with both methods if intronic sequences are included in nuclear RNA-seq analysis. More transcripts are detected in individual whole cells (∼11,000 genes) than nuclei (∼7,000 genes), but the majority of genes have similar detection across cells and nuclei. We estimate that the nuclear proportion of total cellular mRNA varies from 20% to over 50% for large and small pyramidal neurons, respectively. Together, these results illustrate the high information content of nuclear RNA for characterization of cellular diversity in brain tissues.

scholarly journals Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids

2019 ◽  
Author(s):  
Lisa M. Smits ◽  
Stefano Magni ◽  
Kamil Grzyb ◽  
Paul MA. Antony ◽  
Rejko Krüger ◽  
...  
Keyword(s):  
Single Cell ◽  
Dopaminergic Neurons ◽  
Neuronal Cell ◽  
Cell Types ◽  
Human Stem Cell ◽  
Glutamatergic Neurons ◽  
And Function ◽  
Excellent Tool

AbstractHuman stem cell-derived organoids have great potential for modelling physiological and pathological processes. They recapitulatein vitrothe organisation and function of a respective organ or part of an organ. Human midbrain organoids (hMOs) have been described to contain midbrain-specific dopaminergic neurons that release the neurotransmitter dopamine. However, the human midbrain contains also additional neuronal cell types, which are functionally interacting with each other. Here, we analysed hMOs at high-resolution by means of single-cell RNA-sequencing (scRNA-seq), imaging and electrophysiology to unravel cell heterogeneity. Our findings demonstrate that hMOs show essential neuronal functional properties as spontaneous electrophysiological activity of different neuronal subtypes, including dopaminergic, GABAergic, and glutamatergic neurons. Recapitulating thesein vivofeatures makes hMOs an excellent tool forin vitrodisease phenotyping and drug discovery.

scholarly journals Complexity and graded regulation of neuronal cell type-specific alternative splicing revealed by single-cell RNA sequencing

2021 ◽  
Author(s):  
Huijuan Feng ◽  
Daniel F. Moakley ◽  
Shuonan Chen ◽  
Melissa G. McKenzie ◽  
Vilas Menon ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Neuronal Cell ◽  
Cell Types ◽  
Mammalian Brain ◽  
Differential Splicing ◽  
Hierarchical Levels ◽  
Neuronal Types ◽  
And Function

AbstractThe enormous neuronal cellular diversity in the mammalian brain, which is highly prototypical and organized in a hierarchical manner, is dictated by cell type-specific gene regulatory programs at the molecular level. Although prevalent in the brain, contribution of alternative splicing (AS) to the molecular diversity across neuronal cell types is just starting to emerge. Here we systematically investigated AS regulation across over 100 transcriptomically defined neuronal types of the adult mouse cortex using deep single cell RNA-sequencing (scRNA-seq) data. We found distinct splicing programs between glutamatergic and GABAergic neurons and between subclasses within each neuronal class, consisting of overlapping sets of alternative exons showing differential splicing at multiple hierarchical levels. Using an integrative approach, our analysis suggests that RNA-binding proteins (RBPs) Celf1/2, Mbnl2 and Khdrbs3 are preferentially expressed and more active in glutamatergic neurons, while Elavl2 and Qk are preferentially expressed and more active in GABAergic neurons. Importantly, these and additional RBPs also contribute to differential splicing between neuronal subclasses at multiple hierarchical levels, and some RBPs drive splicing dynamics that do not conform to the hierarchical structure defined by the transcriptional profiles. Thus, our results suggest graded regulation of AS across neuronal cell types, which provides a molecular mechanism orthogonal to, rather than downstream of, transcriptional regulation in specifying neuronal identity and function.SignificanceAlternative splicing (AS) is extensively used in the mammalian brain, but its contribution to the molecular and cellular diversity across neuronal cell types remains poorly understood. Through systematic and integrative analysis of AS regulation across over 100 transcriptomically defined cortical neuronal types, we found neuronal subclass-specific splicing regulatory programs consists of overlapping alternative exons showing differential splicing at multiple hierarchical levels. This graded AS regulation is controlled by unique combinations of RNA-binding proteins (RBPs). Importantly, these RBPs also drive splicing dynamics across neuronal cell types that do not conform to the hierarchical taxonomy established based on transcriptional profiles, suggesting that the graded AS regulation provides a molecular mechanism orthogonal to transcriptional regulation in specifying neuronal identity and function.

scholarly journals Cross-species Transcriptomic Comparison of In Vitro and In Vivo Mammalian Neural Cells

2015 ◽  
Vol 9 ◽  
pp. BBI.S33124 ◽  
Author(s):  
Peter R. LoVerso ◽  
Christopher M. Wachter ◽  
Feng Cui
Keyword(s):  
Gene Expression ◽  
Transcript Abundance ◽  
Cell Types ◽  
Mammalian Brain ◽  
Neural Cells ◽  
Rna Seq ◽  
Commercial Sources ◽  
And Function

The mammalian brain is characterized by distinct classes of cells that differ in morphology, structure, signaling, and function. Dysregulation of gene expression in these cell populations leads to various neurological disorders. Neural cells often need to be acutely purified from animal brains for research, which requires complicated procedure and specific expertise. Primary culture of these cells in vitro is a viable alternative, but the differences in gene expression of cells grown in vitro and in vivo remain unclear. Here, we cultured three major neural cell classes of rat brain (ie, neurons, astrocytes, and oligodendrocyte precursor cells [OPCs]) obtained from commercial sources. We measured transcript abundance of these cell types by RNA sequencing (RNA-seq) and compared with their counterparts acutely purified from mouse brains. Cross-species RNA-seq data analysis revealed hundreds of genes that are differentially expressed between the cultured and acutely purified cells. Astrocytes have more such genes compared to neurons and OPCs, indicating that signaling pathways are greatly perturbed in cultured astrocytes. This dataset provides a powerful resource to demonstrate the similarities and differences of biological processes in mammalian neural cells grown in vitro and in vivo at the molecular level.

scholarly journals Single-cell RNA-seq landscape midbrain cell responses to red spotted grouper nervous necrosis virus infection

2021 ◽  
Vol 17 (6) ◽  
pp. e1009665
Author(s):  
Qing Wang ◽  
Cheng Peng ◽  
Min Yang ◽  
Fengqi Huang ◽  
Xuzhuo Duan ◽  
...  
Keyword(s):  
Single Cell ◽  
Immune Cells ◽  
Neuronal Cell ◽  
Cell Types ◽  
Infected Fish ◽  
Nerve Tissue ◽  
Nervous Necrosis Virus ◽  
Epinephelus Coioides ◽  
Rna Seq ◽  
Necrosis Virus

Viral nervous necrosis (VNN) is an acute and serious fish disease caused by nervous necrosis virus (NNV) which has been reported massive mortality in more than fifty teleost species worldwide. VNN causes damage of necrosis and vacuolation to central nervous system (CNS) cells in fish. It is difficult to identify the specific type of cell targeted by NNV, and to decipher the host immune response because of the functional diversity and highly complex anatomical and cellular composition of the CNS. In this study, we found that the red spotted grouper NNV (RGNNV) mainly attacked the midbrain of orange-spotted grouper (Epinephelus coioides). We conducted single-cell RNA-seq analysis of the midbrain of healthy and RGNNV-infected fish and identified 35 transcriptionally distinct cell subtypes, including 28 neuronal and 7 non-neuronal cell types. An evaluation of the subpopulations of immune cells revealed that macrophages were enriched in RGNNV-infected fish, and the transcriptional profiles of macrophages indicated an acute cytokine and inflammatory response. Unsupervised pseudotime analysis of immune cells showed that microglia transformed into M1-type activated macrophages to produce cytokines to reduce the damage to nerve tissue caused by the virus. We also found that RGNNV targeted neuronal cell types was GLU1 and GLU3, and we found that the key genes and pathways by which causes cell cytoplasmic vacuoles and autophagy significant enrichment, this may be the major route viruses cause cell death. These data provided a comprehensive transcriptional perspective of the grouper midbrain and the basis for further research on how viruses infect the teleost CNS.

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