scholarly journals Whole-organism cellular gene-expression atlas reveals conserved cell types in the ventral nerve cord of Platynereis dumerilii

2017 ◽  
Vol 114 (23) ◽  
pp. 5878-5885 ◽  
Author(s):  
Hernando Martínez Vergara ◽  
Paola Yanina Bertucci ◽  
Peter Hantz ◽  
Maria Antonietta Tosches ◽  
Kaia Achim ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Nerve Cord ◽  
Ventral Nerve Cord ◽  
Cell Types ◽  
Animal Evolution ◽  
Mapping Algorithm ◽  
Differentiated Cells ◽  
Rich Diversity ◽  
Platynereis Dumerilii ◽  
Expression Atlas

The comparative study of cell types is a powerful approach toward deciphering animal evolution. To avoid selection biases, however, comparisons ideally involve all cell types present in a multicellular organism. Here, we use image registration and a newly developed “Profiling by Signal Probability Mapping” algorithm to generate a cellular resolution 3D expression atlas for an entire animal. We investigate three-segmented young worms of the marine annelid Platynereis dumerilii, with a rich diversity of differentiated cells present in relatively low number. Starting from whole-mount expression images for close to 100 neural specification and differentiation genes, our atlas identifies and molecularly characterizes 605 bilateral pairs of neurons at specific locations in the ventral nerve cord. Among these pairs, we identify sets of neurons expressing similar combinations of transcription factors, located at spatially coherent anterior-posterior, dorsal-ventral, and medial-lateral coordinates that we interpret as cell types. Comparison with motor and interneuron types in the vertebrate neural tube indicates conserved combinations, for example, of cell types cospecified by Gata1/2/3 and Tal transcription factors. These include V2b interneurons and the central spinal fluid-contacting Kolmer-Agduhr cells in the vertebrates, and several neuron types in the intermediate ventral ganglionic mass in the annelid. We propose that Kolmer-Agduhr cell-like mechanosensory neurons formed part of the mucociliary sole in protostome-deuterostome ancestors and diversified independently into several neuron types in annelid and vertebrate descendants.

scholarly journals A single-cell transcriptomic atlas of the adult Drosophila ventral nerve cord

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Aaron M Allen ◽  
Megan C Neville ◽  
Sebastian Birtles ◽  
Vincent Croset ◽  
Christoph Daniel Treiber ◽  
...  
Keyword(s):  
Single Cell ◽  
Nerve Cord ◽  
Ventral Nerve Cord ◽  
Sensory Information ◽  
Neuronal Cell ◽  
Cell Types ◽  
Distinct Cell ◽  
Old Adult ◽  
And Behavior ◽  
The Brain

The Drosophila ventral nerve cord (VNC) receives and processes descending signals from the brain to produce a variety of coordinated locomotor outputs. It also integrates sensory information from the periphery and sends ascending signals to the brain. We used single-cell transcriptomics to generate an unbiased classification of cellular diversity in the VNC of five-day old adult flies. We produced an atlas of 26,000 high-quality cells, representing more than 100 transcriptionally distinct cell types. The predominant gene signatures defining neuronal cell types reflect shared developmental histories based on the neuroblast from which cells were derived, as well as their birth order. The relative position of cells along the anterior-posterior axis could also be assigned using adult Hox gene expression. This single-cell transcriptional atlas of the adult fly VNC will be a valuable resource for future studies of neurodevelopment and behavior.

scholarly journals Tannic acid-stained microtubules with 12, 13, and 15 protofilaments

1975 ◽  
Vol 65 (1) ◽  
pp. 227-233 ◽  
Author(s):  
PR Burton ◽  
RE Hinkley ◽  
GB Pierson
Keyword(s):  
Cross Section ◽  
Tannic Acid ◽  
Nerve Cord ◽  
Ventral Nerve Cord ◽  
Cell Types ◽  
Subunit Structure ◽  
Meristematic Cells ◽  
Sectioned Material ◽  
Cytoplasmic Microtubules ◽  
Neuronal Systems

Subunit structure in the walls of sectioned microtubules was first noted by Ledbetter and Porter (6), who clearly showed that certain microtubules of plant meristematic cells have 13 wall protofilaments when seen in cross section. Earlier, protofilaments of microtubular elements had been described in negatively stained material, although exact counts of their number were difficult to obtain. In microtubular elements of axonemes, some success has been achieved in visualizing protofilaments in conventionally fixed and sectioned material (8, 10); much less success has been achieved in identifying and counting protofilaments of singlet cytoplasmic microtubules. By using glutaraldehyde-tannic acid fixation, as described by Misuhira and Futaesaku (7), Tilney et al. (12) studied microtubules from a number of sources and found that all have 13 protofilaments comprising their walls. These authors note that "...the number of subunits and their arrangement as protofilaments appear universal...". Preliminary studies of ventral nerve cord of crayfish fixed in glutaraldehyde-tannic acid indicated that axonal microtubules in this material possess only 12 protofilaments (4). On the basis of this observation, tannic acid preparations of several other neuronal and non-neuronal systems were examined. Protofilaments in microtubules from these several cell types are clearly demonstrated, and counts have been made which show that some kinds of microtubules have more or fewer protofilaments than the usual 13 and that at least one kind of microtubule has an even rather than an odd number.

scholarly journals Krüppel-like factor gene function in the ctenophore Mnemiopsis leidyi assessed by CRISPR/Cas9-mediated genome editing

2019 ◽  
Author(s):  
Jason S Presnell ◽  
William E Browne
Keyword(s):  
Transcription Factors ◽  
Genome Editing ◽  
Gene Function ◽  
Functional Role ◽  
Cell Types ◽  
Mnemiopsis Leidyi ◽  
Morpholino Oligonucleotide ◽  
Animal Evolution ◽  
Animal Development ◽  
Summary Statement

AbstractThe Krüppel-like factor (Klf) gene family encodes for transcription factors that play an important role in the regulation of stem cell proliferation, cell differentiation, and development in bilaterians. While Klf genes have been shown to be expressed in various cell types in non-bilaterian animals, their functional role in early diverging animal lineages has not been assessed. Thus, the ancestral activity of these transcription factors in animal development is not well understood. The ctenophore Mnemiopsis leidyi has emerged as an important non-bilaterian model system for understanding early animal evolution. Here we characterize the expression and functional role of Klf genes during M. leidyi embryogenesis. Zygotic Klf gene function was assessed with both CRISPR/Cas9-mediated genome editing knockout and splice-blocking morpholino oligonucleotide knockdown approaches. Abrogation of zygotic Klf expression during M. leidyi embryogenesis results in the irregular development of several organs including the pharynx, tentacle bulbs, and apical organ. Our data suggest an ancient role for Klf genes in regulating endodermal patterning.Summary StatementUsing morpholino oligonucleotide knockdown and CRISPR/Cas9 genome editing, this study shows that in the ctenophore Mnemiopsis leidyi, tissues derived from the endoderm are dependent upon Klf5 ortholog expression for proper development and patterning.

scholarly journals Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Kazuhiro R Nitta ◽  
Arttu Jolma ◽  
Yimeng Yin ◽  
Ekaterina Morgunova ◽  
Teemu Kivioja ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Binding Specificity ◽  
Cell Types ◽  
Regulatory Elements ◽  
Relative Importance ◽  
Specific Expression ◽  
Differentiated Cells ◽  
In Cis ◽  
Human And Mouse

Divergent morphology of species has largely been ascribed to genetic differences in the tissue-specific expression of proteins, which could be achieved by divergence in cis-regulatory elements or by altering the binding specificity of transcription factors (TFs). The relative importance of the latter has been difficult to assess, as previous systematic analyses of TF binding specificity have been performed using different methods in different species. To address this, we determined the binding specificities of 242 Drosophila TFs, and compared them to human and mouse data. This analysis revealed that TF binding specificities are highly conserved between Drosophila and mammals, and that for orthologous TFs, the similarity extends even to the level of very subtle dinucleotide binding preferences. The few human TFs with divergent specificities function in cell types not found in fruit flies, suggesting that evolution of TF specificities contributes to emergence of novel types of differentiated cells.

Stem cells

2019 ◽  
pp. 191-204
Author(s):  
John C. Lucchesi
Keyword(s):  
Stem Cells ◽  
Transcription Factors ◽  
Embryonic Stem ◽  
Cell Types ◽  
Niche Differentiation ◽  
Pluripotent Cells ◽  
Differentiated Cells ◽  
Multipotent Progenitor Cells ◽  
Topological Organization ◽  
Different Cell Types

The zygote and the very early cells are totipotent because they can produce a whole organism. Later, cells become pluripotent because they can differentiate into different subgroups of tissues. These cells can be extracted as embryonic stem cells (ESCs). Their pluripotent nature is due to the action of the pioneer transcription factors Oct4, Sox2 and Nanog. Multipotent or progenitor stem cells are present in adult organisms where they can differentiate into the various cells present in specific tissues. Differentiation depends on their microenvironment or niche. Differentiation of stem cells requires the silencing of the pluripotency genes and the activation of genes that are characteristic of different cell types. The genome of stem cells exhibits the same features of topological organization that are found in somatic cells. At the onset and throughout differentiation, the topological organization of the ESC genome changes, reflecting the changes in transcriptional activity that underlie the progression of pluripotent cells to multipotent progenitor cells and then to differentiated cells.

scholarly journals A single-cell transcriptomic atlas of the adult Drosophila ventral nerve cord

2019 ◽  
Author(s):  
Aaron M. Allen ◽  
Megan C. Neville ◽  
Sebastian Birtles ◽  
Vincent Croset ◽  
Christoph D. Treiber ◽  
...  
Keyword(s):  
Single Cell ◽  
Nerve Cord ◽  
Ventral Nerve Cord ◽  
Sensory Information ◽  
Neuronal Cell ◽  
Cell Types ◽  
Distinct Cell ◽  
Old Adult ◽  
And Behavior ◽  
The Brain

AbstractThe Drosophila ventral nerve cord (VNC) receives and processes descending signals from the brain to produce a variety of coordinated locomotor outputs. It also integrates sensory information from the periphery and sends ascending signals to the brain. We used single-cell transcriptomics to generate an unbiased classification of cellular diversity in the VNC of five-day old adult flies. We produced an atlas of 26,000 high-quality cells, representing more than 100 transcriptionally distinct cell types. The predominant gene signatures defining neuronal cell types reflect shared developmental histories based on the neuroblast from which cells were derived, as well as their birth order. Cells could also be assigned to specific neuromeres using adult Hox gene expression. This single-cell transcriptional atlas of the adult fly VNC will be a valuable resource for future studies of neurodevelopment and behavior.

scholarly journals Single-cell chromatin and gene-regulatory dynamics of mouse nephron progenitors

2021 ◽  
Author(s):  
Sylvia Hilliard ◽  
Giovane Tortelote ◽  
Hongbing Liu ◽  
Chao-Hui Chen ◽  
Samir S El-Dahr
Keyword(s):  
Transcription Factors ◽  
Single Cell ◽  
Cell Fate ◽  
Cell Types ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Bulk Analysis ◽  
Disease States ◽  
Differentiated Cells ◽  
Nephron Progenitors

Background: Cis-regulatory elements (CREs), such as enhancers and promoters, and their cognate transcription factors play a central role in cell fate specification. Bulk analysis of CREs has provided insights into gene regulation in nephron progenitor cells (NPCs). However, the cellular resolution required to unravel the dynamic changes in regulatory elements associated with cell fate choices remains to be defined. Methods: We integrated single-cell chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) in embryonic E16.5 (self-renewing) and postnatal P2 (primed) mouse Six2GFP NPCs. This analysis revealed NPC diversity and identified candidate CREs. To validate these findings and gain additional insights into more differentiated cell types, we performed a multiome analysis of E16.5 and P2 kidneys. Results: CRE accessibility recovered the diverse states of NPCs and precursors of differentiated cells. Single-cell types such as podocytes, proximal and distal precursors are marked by differentially accessible CREs. Domains of regulatory chromatin as defined by rich CRE-gene associations identified NPC fate-determining transcription factors (TF). Likewise, key TF expression correlates well with its regulon activity. Young NPCs exhibited enrichment in accessible motifs for bHLH, homeobox, and Forkhead TFs, while older NPCs were enriched in AP-1, HNF1, and HNF4 motif activity. A subset of Forkhead factors exhibiting high chromatin activity in podocyte precursors. Conclusion: Defining the regulatory landscape of nephrogenesis at single-cell resolution informs the basic mechanisms of nephrogenesis and provides a foundation for future studies in disease states characterized by abnormal nephrogenesis.

scholarly journals Krüppel-like factor gene function in the ctenophore Mnemiopsis leidyi assessed by CRISPR/Cas9-mediated genome editing

Development ◽  
2021 ◽  
Author(s):  
Jason S. Presnell ◽  
William E. Browne
Keyword(s):  
Cell Proliferation ◽  
Transcription Factors ◽  
Genome Editing ◽  
Gene Function ◽  
Cell Types ◽  
Abnormal Development ◽  
Mnemiopsis Leidyi ◽  
Animal Evolution ◽  
Animal Development

The Krüppel-like factor (Klf) gene family encodes for transcription factors that play an important role in the regulation of stem cell proliferation, cell differentiation, and development in bilaterians. While Klf genes have been shown to functionally specify various cell types in non-bilaterian animals, their role in early diverging animal lineages has not been assessed. Thus, the ancestral activity of these transcription factors in animal development is not well understood. The ctenophore Mnemiopsis leidyi has emerged as an important non-bilaterian model system for understanding early animal evolution. Here we characterize the expression and functional role of Klf genes during M. leidyi embryogenesis. Zygotic Klf gene function was assessed with both CRISPR/Cas9-mediated genome editing and splice-blocking morpholino oligonucleotide knockdown approaches. Abrogation of zygotic Klf expression during M. leidyi embryogenesis results in abnormal development of several organs including the pharynx, tentacle bulbs, and apical organ. Our data suggest an ancient role for Klf genes in regulating endodermal patterning, possibly through regulation of cell proliferation.

Extracellular filaments in the perineurium of the florida lobster, Panulirus argus

1987 ◽  
Vol 45 ◽  
pp. 784-785
Author(s):  
Roy J. Baerwald ◽  
Lura C. Williamson
Keyword(s):  
Blood Brain Barrier ◽  
Glial Cells ◽  
Tannic Acid ◽  
Nerve Cord ◽  
Ventral Nerve Cord ◽  
Florida Keys ◽  
Panulirus Argus ◽  
Brain Barrier ◽  
Cacodylate Buffer ◽  
Nerve Cords

In arthropods the perineurium surrounds the neuropile, consists of modified glial cells, and is the morphological basis for the blood-brain barrier. The perineurium is surrounded by an acellular neural lamella, sometimes containing scattered collagen-like fibrils. This perineurial-neural lamellar complex is thought to occur ubiquitously throughout the arthropods. This report describes a SEM and TEM study of the sheath surrounding the ventral nerve cord of Panulirus argus.Juvenile P. argus were collected from the Florida Keys and maintained in marine aquaria. Nerve cords were fixed for TEM in Karnovsky's fixative and saturated tannic acid in 0.1 M Na-cacodylate buffer, pH = 7.4; post-fixed in 1.0% OsO4 in the same buffer; dehydrated through a graded series of ethanols; embedded in Epon-Araldite; and examined in a Philips 200 TEM. Nerve cords were fixed for SEM in a similar manner except that tannic acid was not used.

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