scholarly journals Atlas of Neuromuscular Organization in the Ctenophore, Pleurobrachia bachei (A. Agassiz, 1860)

2018 ◽  
Author(s):  
Leonid L Moroz ◽  
Tigran P Norekian
Keyword(s):  
Prey Capture ◽  
Parallel Evolution ◽  
Cell Types ◽  
Neural System ◽  
Cell Type ◽  
Nervous Systems ◽  
Surface Receptors ◽  
Basal Metazoan ◽  
Pleurobrachia Bachei ◽  
Type Specification

Enigmatic ctenophores are descendants of one of the earliest branching metazoan lineage. Their nervous systems are equally elusive. The lack of convenient neurogenic molecules and neurotransmitters suggests an extensive parallel evolution and independent origins of neurons and synapses. However, the field is logged behind due to the lack of microanatomical data about the neuro-muscular systems in this group of animals. Here, using immunohistochemistry and scanning electron microscopy, we describe the organization of both muscular and nervous systems in the sea gooseberry, Pleurobrachia bachei, from North Pacific. The diffused neural system of Pleurobrachia consists of two subsystems: the subepithelial neural network and the mesogleal net with about 5000-7000 neurons combined. Our data revealed the unprecedented complexity of neuromuscular organization in this basal metazoan lineage. The anatomical diversity of cell types includes at least nine broad categories of neurons, five families of surface receptors and more than two dozen types of muscle cells as well as regional concentrations of neuronal elements to support ctenophore feeding, complex swimming, escape and prey capture behaviors. In summary, we recognize more than 80 total morphological cell types. Thus, in terms of cell type specification and diversity, ctenophores significantly exceed what we currently know about other prebilaterian groups (placozoan, sponges, and cnidarians), and some basal bilaterians.

scholarly journals A cis-regulatory atlas in maize at single-cell resolution

2020 ◽  
Author(s):  
Alexandre P. Marand ◽  
Zongliang Chen ◽  
Andrea Gallavotti ◽  
Robert J. Schmitz
Keyword(s):  
Single Cell ◽  
Cell Types ◽  
Regulatory Elements ◽  
Cellular Heterogeneity ◽  
Cell Type ◽  
Crop Species ◽  
Cell Functions ◽  
Cell Type Specific ◽  
Type Specification ◽  
Accessible Chromatin

ABSTRACTCis-regulatory elements (CREs) encode the genomic blueprints for coordinating spatiotemporal gene expression programs underlying highly specialized cell functions. To identify CREs underlying cell-type specification and developmental transitions, we implemented single-cell sequencing of Assay for Transposase Accessible Chromatin in an atlas of Zea mays organs. We describe 92 distinct states of chromatin accessibility across more than 165,913 putative CREs, 56,575 cells, and 52 known cell-types in maize using a novel implementation of regularized quasibinomial logistic regression. Cell states were largely determined by combinatorial accessibility of transcription factors (TFs) and their binding sites. A neural network revealed that cell identity could be accurately predicted (>0.94) solely based on TF binding site accessibility. Co-accessible chromatin recapitulated higher-order chromatin interactions, with distinct sets of TFs coordinating cell type-specific regulatory dynamics. Pseudotime reconstruction and alignment with Arabidopsis thaliana trajectories identified conserved TFs, associated motifs, and cis-regulatory regions specifying sequential developmental progressions. Cell-type specific accessible chromatin regions were enriched with phenotype-associated genetic variants and signatures of selection, revealing the major cell-types and putative CREs targeted by modern maize breeding. Collectively, our analysis affords a comprehensive framework for understanding cellular heterogeneity, evolution, and cis-regulatory grammar of cell-type specification in a major crop species.

scholarly journals Notch signalling patterns retinal composition by regulating atoh7 during post-embryonic growth

2018 ◽  
Author(s):  
Alicia Pérez Saturnino ◽  
Katharina Lust ◽  
Joachim Wittbrodt
Keyword(s):  
De Novo ◽  
Cell Types ◽  
Notch Signalling ◽  
Cell Type ◽  
Lineage Specification ◽  
Cell Type Composition ◽  
Type Composition ◽  
Cell Niche ◽  
Functional Relevance ◽  
Type Specification

AbstractPatterning of a continuously growing naive field in the context of a life-long growing organ, the teleost eye is of highest functional relevance. Intrinsic and extrinsic signals were proposed to regulate lineage specification in progenitors that exit the stem cell niche in the ciliary marginal zone (CMZ). The proper cell type composition arising from those progenitors is prerequisite for retinal function. Our findings in the teleost medaka (Oryzias latipes) uncover that the Notch–Atoh7 axis continuously patterns the CMZ. The complement of cell-types originating from the two juxtaposed progenitors marked by Notch or Atoh7 activity contains all constituents of a retinal column. Modulation of Notch signalling specifically in Atoh7-expressing cells demonstrates the crucial role of this axis in generating the correct cell type proportions. After transiently blocking Notch signalling, retinal patterning and differentiation is reinitiated de novo. Taken together we show that Notch activity in the CMZ continuously structures the growing retina by juxtaposing Notch and Atoh7 progenitors giving rise to distinct, complementary lineages, revealing a coupling of de novo patterning and cell-type specification in the respective lineages.

scholarly journals Gene Signature of the Human Pancreatic ε Cell

Endocrinology ◽  
2018 ◽  
Vol 159 (12) ◽  
pp. 4023-4032 ◽  
Author(s):  
Giselle Dominguez Gutierrez ◽  
Jinrang Kim ◽  
Ann-Hwee Lee ◽  
Jenny Tong ◽  
JingJing Niu ◽  
...  
Keyword(s):  
Endocrine Cell ◽  
Metabolic Pathways ◽  
Cell Types ◽  
Gene Signature ◽  
Human Islet ◽  
Cell Type ◽  
Sequencing Technology ◽  
Surface Receptors ◽  
Molecular Features ◽  
Endocrine Cell Type

Abstract The ghrelin-producing ε cell represents the fifth endocrine cell type in human pancreatic islets. The abundance of ε cells in adult pancreas is extremely low, which has hampered the investigation on the molecular pathways regulating the development and the function of this cell type. In this study, we explored the molecular features defining the function of pancreatic ε cells isolated from adult nondiabetic donors using single-cell RNA sequencing technology. We focus on transcription factors, cell surface receptors, and genes involved in metabolic pathways that contribute to regulation of cellular function. Furthermore, the genes that separate ε cells from the other islet endocrine cell types are presented. This study expands prior knowledge about the genes important for ε cell functioning during development and provides a resource to interrogate the transcriptome of this rare human islet cell type.

Tissue layer and organ specificity of trichome formation are regulated by GLABRA1 and TRIPTYCHON in Arabidopsis

Development ◽  
1998 ◽  
Vol 125 (12) ◽  
pp. 2283-2289 ◽  
Author(s):  
A. Schnittger ◽  
G. Jurgens ◽  
M. Hulskamp
Keyword(s):  
Cell Types ◽  
Negative Regulator ◽  
Organ Specificity ◽  
Cell Type ◽  
Tissue Layer ◽  
Germ Layers ◽  
Animal Development ◽  
Spatial Regulation ◽  
Trichome Formation ◽  
Type Specification

In animal development, cellular diversity is generated within tissues which in turn are derived from germ layers. Similar to the germ layers in animals, plants establish three distinct tissue layers early in development which each give rise to a distinct set of cell types. To investigate the role of tissue-layer-specific cues in generating plant cellular diversity we studied the spatial regulation of an epidermal cell type, trichomes (hairs), by the two genes, GLABRA1 (GL1) and TRIPTYCHON (TRY). Ubiquitous expression of the positive regulator GL1 in the absence of the negative regulator TRY leads to ectopic trichome formation not only on additional organs but also in subepidermal tissue layers. Trichomes in inner tissue layers can differentiate the same morphology and show a spacing pattern comparable to trichomes in the epidermis. This clearly shows that cell type specification takes place downstream of tissue-specific cues. We propose a model of how the tissue and organ specificity of trichome induction is regulated in normal development.

scholarly journals How a cell decides its own fate: a single-cell view of molecular mechanisms and dynamics of cell-type specification

2021 ◽  
Author(s):  
Maria Mircea ◽  
Stefan Semrau
Keyword(s):  
Single Cell ◽  
Molecular Mechanisms ◽  
Cell Types ◽  
Lineage Tracing ◽  
Molecular Profile ◽  
Cell Type ◽  
Molecular Changes ◽  
Starting Point ◽  
A Cell ◽  
Type Specification

On its path from a fertilized egg to one of the many cell types in a multicellular organism, a cell turns the blank canvas of its early embryonic state into a molecular profile fine-tuned to achieve a vital organismal function. This remarkable transformation emerges from the interplay between dynamically changing external signals, the cell's internal, variable state, and tremendously complex molecular machinery; we are only beginning to understand. Recently developed single-cell omics techniques have started to provide an unprecedented, comprehensive view of the molecular changes during cell-type specification and promise to reveal the underlying gene regulatory mechanism. The exponentially increasing amount of quantitative molecular data being created at the moment is slated to inform predictive, mathematical models. Such models can suggest novel ways to manipulate cell types experimentally, which has important biomedical applications. This review is meant to give the reader a starting point to participate in this exciting phase of molecular developmental biology. We first introduce some of the principal molecular players involved in cell-type specification and discuss the important organizing ability of biomolecular condensates, which has been discovered recently. We then review some of the most important single-cell omics methods and relevant findings they produced. We devote special attention to the dynamics of the molecular changes and discuss methods to measure them, most importantly lineage tracing. Finally, we introduce a conceptual framework that connects all molecular agents in a mathematical model and helps us make sense of the experimental data.

scholarly journals Orthogonal activation of metabotropic glutamate receptor using coordination chemogenetics

2021 ◽  
Author(s):  
Akinobu Senoo ◽  
Yutaro Yamada ◽  
Kento Ojima ◽  
Tomohiro Doura ◽  
Itaru Hamachi ◽  
...  
Keyword(s):  
Glutamate Receptor ◽  
Protein Design ◽  
Metal Ion ◽  
Metabotropic Glutamate Receptor ◽  
Cell Types ◽  
Hek293 Cells ◽  
Cell Type ◽  
Surface Receptors ◽  
Metabotropic Glutamate ◽  
Metabotropic Glutamate Receptor 1

Cell-surface receptors play a pivotal role as transducers of extracellular input. Although different cell types express the same receptor, the physiological roles of the receptor are highly dependent on cell type. To understand each role, tactics for cell-specific activation of the target receptor are in high demand. Herein, we developed an orthogonal activation method targeting metabotropic glutamate receptor 1 (mGlu1), a G-protein coupled receptor. In this method, direct activation via coordination-based chemogenetics (dA-CBC) was adopted, where activation of mGlu1 was artificially induced by a protein conformational change in response to the coordination of a metal ion or metal-ion complex. Our structure-based protein design and screening approach identified mGlu1 mutants that were directly activated by the coordination of Cu2+ or Zn2+, in addition to our previous Pd-complex-sensitive mGlu1 mutant. Notably, the activation of the mutants was mutually orthogonal, resulting in cell-type selective activation in a model system using HEK293 cells.

scholarly journals Orthogonal Activation of Metabotropic Glutamate Receptor Using Coordination Chemogenetics

2022 ◽  
Vol 9 ◽  
Author(s):  
Akinobu Senoo ◽  
Yutaro Yamada ◽  
Kento Ojima ◽  
Tomohiro Doura ◽  
Itaru Hamachi ◽  
...  
Keyword(s):  
Glutamate Receptor ◽  
Protein Design ◽  
Metal Ion ◽  
Metabotropic Glutamate Receptor ◽  
Cell Types ◽  
Hek293 Cells ◽  
Cell Type ◽  
Surface Receptors ◽  
Metabotropic Glutamate ◽  
Metabotropic Glutamate Receptor 1

Cell-surface receptors play a pivotal role as transducers of extracellular input. Although different cell types express the same receptor, the physiological roles of the receptor are highly dependent on cell type. To understand each role, tactics for cell-specific activation of the target receptor are in high demand. Herein, we developed an orthogonal activation method targeting metabotropic glutamate receptor 1 (mGlu1), a G-protein coupled receptor. In this method, direct activation via coordination-based chemogenetics (dA-CBC) was adopted, where activation of mGlu1 was artificially induced by a protein conformational change in response to the coordination of a metal ion or metal-ion complex. Our structure-based protein design and screening approach identified mGlu1 mutants that were directly activated by the coordination of Cu2+ or Zn2+, in addition to our previous Pd-complex-sensitive mGlu1 mutant. Notably, the activation of the mutants was mutually orthogonal, resulting in cell-type selective activation in a model system using HEK293 cells.

scholarly journals Lineage-specific control of convergent differentiation by a Forkhead repressor

2019 ◽  
Author(s):  
Karolina Mizeracka ◽  
Julia M. Rogers ◽  
Jonathan D. Rumley ◽  
Shai Shaham ◽  
Martha L. Bulyk ◽  
...  
Keyword(s):  
Cell Types ◽  
Human Homolog ◽  
Cell Type ◽  
Forkhead Transcription Factor ◽  
C Elegans ◽  
Identical Cell ◽  
Cell Type Specific ◽  
Activate Cell ◽  
Type Specification ◽  
Specific Control

ABSTRACTDuring convergent differentiation, multiple developmental lineages produce a highly similar or identical cell type. However, the molecular players that drive convergent differentiation are not known. Here, we show that the C. elegans Forkhead transcription factor UNC-130 is required in only one of three convergent lineages that produce the same glial cell type. UNC-130 acts transiently as a repressor in progenitors and newly-born terminal cells to allow the proper specification of cells related by lineage rather than by cell type. Specification defects correlate with UNC-130:DNA binding, and UNC-130 can be functionally replaced by its human homolog, the neural crest lineage determinant FoxD3. We propose that, in contrast to terminal selectors that activate cell-type specific transcriptional programs in terminally differentiating cells, UNC-130 acts earlier to enable molecularly distinct progenitors to produce equivalent cell types. These findings provide evidence that convergent differentiation involves distinct transcriptional paths leading to the same cell type.

scholarly journals A draft network of ligand–receptor-mediated multicellular signalling in human

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Jordan A. Ramilowski ◽  
Tatyana Goldberg ◽  
Jayson Harshbarger ◽  
Edda Kloppmann ◽  
Marina Lizio ◽  
...  
Keyword(s):  
Large Scale ◽  
Cell Communication ◽  
Cell Types ◽  
Cell Type ◽  
Cell Type Specificity ◽  
Surface Receptors ◽  
Signalling Network ◽  
Multiple Cell ◽  
Autocrine Signalling ◽  
Multiple Ligand

Abstract Cell-to-cell communication across multiple cell types and tissues strictly governs proper functioning of metazoans and extensively relies on interactions between secreted ligands and cell-surface receptors. Herein, we present the first large-scale map of cell-to-cell communication between 144 human primary cell types. We reveal that most cells express tens to hundreds of ligands and receptors to create a highly connected signalling network through multiple ligand–receptor paths. We also observe extensive autocrine signalling with approximately two-thirds of partners possibly interacting on the same cell type. We find that plasma membrane and secreted proteins have the highest cell-type specificity, they are evolutionarily younger than intracellular proteins, and that most receptors had evolved before their ligands. We provide an online tool to interactively query and visualize our networks and demonstrate how this tool can reveal novel cell-to-cell interactions with the prediction that mast cells signal to monoblastic lineages via the CSF1–CSF1R interacting pair.

scholarly journals A Single-cell Transcriptomic Atlas of the Developing Chicken Limb

2019 ◽  
Author(s):  
Christian Feregrino ◽  
Fabio Sacher ◽  
Oren Parnas ◽  
Patrick Tschopp
Keyword(s):  
Pattern Formation ◽  
Single Cell ◽  
Rna Sequencing ◽  
Cell Types ◽  
Cell Populations ◽  
Cell Type ◽  
Data Set ◽  
Cellular Resolution ◽  
Single Cell Rna Sequencing ◽  
Type Specification

AbstractBackgroundThrough precise implementation of distinct cell type specification programs, differentially regulated in both space and time, complex patterns emerge during organogenesis. Thanks to its easy experimental accessibility, the developing chicken limb has long served as a paradigm to study vertebrate pattern formation. Through decades’ worth of research, we now have a firm grasp on the molecular mechanisms driving limb formation at the tissue-level. However, to elucidate the dynamic interplay between transcriptional cell type specification programs and pattern formation at its relevant cellular scale, we lack appropriately resolved molecular data at the genome-wide level. Here, making use of droplet-based single-cell RNA-sequencing, we catalogue the developmental emergence of distinct tissue types and their transcriptome dynamics in the distal chicken limb, the so-called autopod, at cellular resolution.ResultsUsing single-cell RNA-sequencing technology, we sequenced a total of 17,628 cells coming from three key developmental stages of chicken autopod patterning. Overall, we identified 23 cell populations with distinct transcriptional profiles. Amongst them were small, albeit essential populations like the apical ectodermal ridge, demonstrating the ability to detect even rare cell types. Moreover, we uncovered the existence of molecularly distinct sub-populations within previously defined compartments of the developing limb, some of which have important signaling functions during autopod pattern formation. Finally, we inferred gene co-expression modules that coincide with distinct tissue types across developmental time, and used them to track patterning-relevant cell populations of the forming digits.ConclusionsWe provide a comprehensive functional genomics resource to study the molecular effectors of chicken limb patterning at cellular resolution. Our single-cell transcriptomic atlas captures all major cell populations of the developing autopod, and highlights the transcriptional complexity in many of its components. Finally, integrating our data-set with other single-cell transcriptomics resources will enable researchers to assess molecular similarities in orthologous cell types across the major tetrapod clades, and provide an extensive candidate gene list to functionally test cell-type-specific drivers of limb morphological diversification.

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