scholarly journals Time and space in segmentation

2021 ◽  
Vol 11 (3) ◽  
Author(s):  
Erik Clark
Keyword(s):  
Spatial Organization ◽  
Spatial Information ◽  
Positional Information ◽  
Coarse Grained ◽  
Scaling Relationships ◽  
Evolutionary Origins ◽  
Developmental Patterning ◽  
Wave Patterns ◽  
Axial Variation ◽  
Oscillator Output

Arthropod segmentation and vertebrate somitogenesis are leading fields in the experimental and theoretical interrogation of developmental patterning. However, despite the sophistication of current research, basic conceptual issues remain unresolved. These include: (i) the mechanistic origins of spatial organization within the segment addition zone (SAZ); (ii) the mechanistic origins of segment polarization; (iii) the mechanistic origins of axial variation; and (iv) the evolutionary origins of simultaneous patterning. Here, I explore these problems using coarse-grained models of cross-regulating dynamical processes. In the morphogenetic framework of a row of cells undergoing axial elongation, I simulate interactions between an ‘oscillator’, a ‘switch’ and up to three ‘timers’, successfully reproducing essential patterning behaviours of segmenting systems. By comparing the output of these largely cell-autonomous models to variants that incorporate positional information, I find that scaling relationships, wave patterns and patterning dynamics all depend on whether the SAZ is regulated by temporal or spatial information. I also identify three mechanisms for polarizing oscillator output, all of which functionally implicate the oscillator frequency profile. Finally, I demonstrate significant dynamical and regulatory continuity between sequential and simultaneous modes of segmentation. I discuss these results in the context of the experimental literature.

scholarly journals Time and Space in Segmentation

2020 ◽  
Author(s):  
Erik Clark
Keyword(s):  
Spatial Information ◽  
Positional Information ◽  
Coarse Grained ◽  
Spatial Organisation ◽  
Scaling Relationships ◽  
Evolutionary Origins ◽  
Developmental Patterning ◽  
Wave Patterns ◽  
Axial Variation ◽  
Oscillator Output

AbstractArthropod segmentation and vertebrate somitogenesis are leading fields in the experimental and theoretical interrogation of developmental patterning. However, despite the sophistication of current research, basic conceptual issues remain unresolved. These include (1) the mechanistic origins of spatial organisation within the segment addition zone (SAZ); (2) the mechanistic origins of segment polarisation; (3) the mechanistic origins of axial variation; and (4) the evolutionary origins of simultaneous patterning. Here, I explore these problems using coarse-grained models of cross-regulating dynamical processes. In the morphogenetic framework of a row of cells undergoing axial elongation, I simulate interactions between an “oscillator”, a “switch”, and up to three “timers”, successfully reproducing essential patterning behaviours of segmenting systems. By comparing the output of these largely cell-autonomous models to variants that incorporate positional information, I find that scaling relationships, wave patterns, and patterning dynamics all depend on whether the SAZ is regulated by temporal or spatial information. I also identify three mechanisms for polarising oscillator output, all of which functionally implicate the oscillator frequency profile. Finally, I demonstrate significant dynamical and regulatory continuity between sequential and simultaneous modes of segmentation. I discuss these results in the context of the experimental literature.

Volumes and Surface Areas: Geometries and Scaling Relationships between Coarse- Grained and Atomic Structures

2014 ◽  
Vol 20 (8) ◽  
pp. 1208-1222 ◽  
Author(s):  
Daniel Flatow ◽  
Sumudu Leelananda ◽  
Aris Skliros ◽  
Andrzej Kloczkowski ◽  
Robert Jernigan
Keyword(s):  
Coarse Grained ◽  
Atomic Structures ◽  
Scaling Relationships ◽  
Surface Areas

scholarly journals A time-stamp mechanism may provide temporal information necessary for egocentric to allocentric spatial transformations

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Avner Wallach ◽  
Erik Harvey-Girard ◽  
James Jaeyoon Jun ◽  
André Longtin ◽  
Len Maler
Keyword(s):  
Spatial Learning ◽  
Spatial Organization ◽  
Spatial Information ◽  
Spatial Relations ◽  
Temporal Information ◽  
Accurate Estimation ◽  
Neural Recordings ◽  
Brain Circuitry ◽  
Learning Circuits ◽  
Thalamic Region

Learning the spatial organization of the environment is essential for most animals’ survival. This requires the animal to derive allocentric spatial information from egocentric sensory and motor experience. The neural mechanisms underlying this transformation are mostly unknown. We addressed this problem in electric fish, which can precisely navigate in complete darkness and whose brain circuitry is relatively simple. We conducted the first neural recordings in the preglomerular complex, the thalamic region exclusively connecting the optic tectum with the spatial learning circuits in the dorsolateral pallium. While tectal topographic information was mostly eliminated in preglomerular neurons, the time-intervals between object encounters were precisely encoded. We show that this reliable temporal information, combined with a speed signal, can permit accurate estimation of the distance between encounters, a necessary component of path-integration that enables computing allocentric spatial relations. Our results suggest that similar mechanisms are involved in sequential spatial learning in all vertebrates.

scholarly journals H3K9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Andrey Poleshko ◽  
Cheryl L Smith ◽  
Son C Nguyen ◽  
Priya Sivaramakrishnan ◽  
Karen G Wong ◽  
...  
Keyword(s):  
Cell Division ◽  
Spatial Organization ◽  
Nuclear Periphery ◽  
Nuclear Lamina ◽  
Positional Information ◽  
Specific Gene ◽  
Cell Type ◽  
Histone 3 ◽  
Spatial Positioning ◽  
Peripheral Heterochromatin

Cell-type-specific 3D organization of the genome is unrecognizable during mitosis. It remains unclear how essential positional information is transmitted through cell division such that a daughter cell recapitulates the spatial genome organization of the parent. Lamina-associated domains (LADs) are regions of repressive heterochromatin positioned at the nuclear periphery that vary by cell type and contribute to cell-specific gene expression and identity. Here we show that histone 3 lysine 9 dimethylation (H3K9me2) is an evolutionarily conserved, specific mark of nuclear peripheral heterochromatin and that it is retained through mitosis. During mitosis, phosphorylation of histone 3 serine 10 temporarily shields the H3K9me2 mark allowing for dissociation of chromatin from the nuclear lamina. Using high-resolution 3D immuno-oligoFISH, we demonstrate that H3K9me2-enriched genomic regions, which are positioned at the nuclear lamina in interphase cells prior to mitosis, re-associate with the forming nuclear lamina before mitotic exit. The H3K9me2 modification of peripheral heterochromatin ensures that positional information is safeguarded through cell division such that individual LADs are re-established at the nuclear periphery in daughter nuclei. Thus, H3K9me2 acts as a 3D architectural mitotic guidepost. Our data establish a mechanism for epigenetic memory and inheritance of spatial organization of the genome.

Cytoskeletal coordination and intercellular signalling during metazoan embryogenesis

Development ◽  
1981 ◽  
Vol 65 (1) ◽  
pp. 1-25
Author(s):  
J. B. Tucker
Keyword(s):  
Cell Surface ◽  
Spatial Organization ◽  
Positional Information ◽  
Animal Tissues ◽  
Marked Contrast ◽  
Cytoskeletal Organization ◽  
Motor Network ◽  
Intercellular Signalling ◽  
Signal Mode ◽  
Spatiotemporal Integration

This article draws attention to certain recently discovered features of cell surface organization and cytoskeletal deployment that may be revealing a new basis for intercellular signalling during metazoan embryogenesis. It is a signal mode that could coordinate many aspects of ‘Entwicklungsmechanik’ by spatiotemporal integration of the cytoskeletal/motor network throughout developing tissues. Evidence that this is achieved by ‘intercellular cytoskeletal/plasma membrane connecting systems’ which coordinate the spatial organization of microtubules, microfilaments, and intermediate filaments in developing animal tissues is critically examined. It is argued that this system does operate but that it is not used to transmit positional information in embryonic fields. However, it probably responds to such information and might play an important part in establishing field boundaries during the very earliest stages of embryogenesis. Certain aspects of cell surface organization in contemporary protozoans reveal ways in which the Protozoa could have been pre-adapted for the employment of cytoskeletal/cell surface signalling during the advent of multicellularity. In marked contrast, such signalling does not appear to be exploited during plant morphogenesis. The extent to which cytoskeletal organization might be coordinated in sisier cells by transmission of spatial instructions during cell division in both animal and plant tissues is also considered.

Development of a Communication Aid App with iOS Devices to Support Children/Persons with Speech Disabilities Improvement in Obtaining Positioning Information with iBeacon as Near Field Radio Communication Technology

2017 ◽  
Vol 21 (2) ◽  
pp. 371-377
Author(s):  
Tomonori Karita ◽  
Keyword(s):  
Correct Answer ◽  
Social Life ◽  
Spatial Information ◽  
Near Field ◽  
Positional Information ◽  
Radio Communication ◽  
Communication Aid ◽  
Research Task ◽  
Speech Disabilities ◽  
Gps System

Communication has such a vital function as the foundation of human social life that speech disabilities can drastically deteriorate people’s quality of life. The author has developed a voice output communication aid (VOCA) to enable children/persons with speech disabilities to communicate with other people according to conversation situations with iOS devices with global positioning system (GPS), positional information acquiring technology (iBeacon), and a clock function installed. The developed technology is an application compatible with iOS (hereinafter, app) that displays a list of messages (hereinafter, VOCA interface) if any of them correspond to the information on the user’s location and time of use as acquired by users with a portable information device with a GPS function, iBeacon function, and clock function installed. Users can communicate by selecting the icons of required messages from VOCA interfaces to reproduce registered voice data instead of their own voices. We have named the developed technology “Friendly VOCA” because its intentions are that: (1) users can communicate with other people with as few operations involved as possible; (2) it should be easy for users to learn and to operate. This paper reports the development processes of the Friendly VOCA and defines the ratios of preregistered VOCA interfaces displayed (hereinafter, correct answer rates) in acquiring positional information with GPS and with iBeacon. In Research Task 1, we have conducted experiments to verify the correct answer rates of the GPS system in outdoor use of the Friendly VOCA and in Research Task 2 we have conducted experiments to verify the correct answer rates of the iBeacon system in indoor use of the Friendly VOCA. The research results show that both the GPS system and iBeacon system can specify user’s spatial information and display appropriate lists of messages. However, the experiments found that iBeacon signal transmitters can transmit signals over a distance of 50 m or more: to improve the correct answer rates of the iBeacon system, we may need to increase the distance between iBeacon signal transmitters or select devices with a shorter range of transmission.

scholarly journals Robust Acquisition of High Resolution Spatial Transcriptomes from Preserved Tissues with Immunofluorescence Based Laser Capture Microdissection

2021 ◽  
Author(s):  
Xiaodan Zhang ◽  
Chuansheng Hu ◽  
Chen Huang ◽  
Ying Wei ◽  
Xiaowei Li ◽  
...  
Keyword(s):  
Laser Capture Microdissection ◽  
Spatial Organization ◽  
Spatial Information ◽  
A Priori ◽  
Rna Degradation ◽  
Spatially Resolved ◽  
Mouse Small Intestine ◽  
Dissociated Cells ◽  
Laser Capture

The functioning of tissues is fundamentally dependent upon not only the phenotypes of the constituent cells but also their spatial organization in the tissue. However, obtaining comprehensive transcriptomic data based on established phenotypes while retaining this spatial information has been challenging. Here we present a general and robust method based on immunofluorescence-guided laser capture microdissection (immuno-LCM-RNAseq) to enable acquisition of finely resolved spatial transcriptomes with as few as tens of cells from snap-frozen or RNAlater-treated tissues, overcoming the long-standing problem of significant RNA degradation during this lengthy process. The efficacy of this approach is exemplified by the characterization of differences at the transcript isoform level between cells at the tip versus the main capillary body of the mouse small intestine lacteal. With the extensive repertoire of phenotype-specific antibodies that are presently available, our method provides a powerful means by which spatially resolved cellular states can be delineated in situ with preserved tissues. Moreover, such high quality spatial transcriptomes defined by immuno-markers can be used to compare with clusters obtained from single-cell RNAseq studies of dissociated cells as well as applied to bead-based spatial transcriptomics approaches that require such information a priori for cell identification.

scholarly journals Localization of T cell clonotypes using spatial transcriptomics

2021 ◽  
Author(s):  
William H. Hudson ◽  
Lisa J. Sudmeier
Keyword(s):  
T Cell ◽  
Spatial Organization ◽  
Spatial Information ◽  
Human Tumor ◽  
Cell Receptor ◽  
Cell Repertoire ◽  
T Cell Clones ◽  
Human T Cell ◽  
Cell Clones ◽  
Archived Samples

Spatial transcriptomics is an emerging technology that measures gene expression while preserving spatial information. Here, we present a method to determine localization of specific T cell clones by obtaining T cell receptor (TCR) sequences from spatial transcriptomics assays. Our method uses an existing commercial spatial transcriptomics platform and open-source software for analysis, allowing simple and inexpensive integration with archived samples and existing laboratory workflows. Using human brain metastasis samples, we show that TCR sequences are readily obtained from human tumor tissue and that these sequences are recapitulated by single-cell sequencing methods. This technique will permit detailed studies of the spatial organization of the human T cell repertoire, such as the identification of tumor- infiltrating and tumor-excluded T cell clones.

scholarly journals Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data

2020 ◽  
Vol 3 (11) ◽  
pp. e202000867 ◽  
Author(s):  
Jovan Tanevski ◽  
Thin Nguyen ◽  
Buu Truong ◽  
Nikos Karaiskos ◽  
Mehmet Eren Ahsen ◽  
...  
Keyword(s):  
Single Cell ◽  
Spatial Organization ◽  
Gene Selection ◽  
Spatial Information ◽  
Spatial Clustering ◽  
Spatial Location ◽  
Spatial Arrangement ◽  
Fish Embryo ◽  
Hybridization Data ◽  
Silver Standard

Single-cell RNA-sequencing (scRNAseq) technologies are rapidly evolving. Although very informative, in standard scRNAseq experiments, the spatial organization of the cells in the tissue of origin is lost. Conversely, spatial RNA-seq technologies designed to maintain cell localization have limited throughput and gene coverage. Mapping scRNAseq to genes with spatial information increases coverage while providing spatial location. However, methods to perform such mapping have not yet been benchmarked. To fill this gap, we organized the DREAM Single-Cell Transcriptomics challenge focused on the spatial reconstruction of cells from the Drosophila embryo from scRNAseq data, leveraging as silver standard, genes with in situ hybridization data from the Berkeley Drosophila Transcription Network Project reference atlas. The 34 participating teams used diverse algorithms for gene selection and location prediction, while being able to correctly localize clusters of cells. Selection of predictor genes was essential for this task. Predictor genes showed a relatively high expression entropy, high spatial clustering and included prominent developmental genes such as gap and pair-rule genes and tissue markers. Application of the top 10 methods to a zebra fish embryo dataset yielded similar performance and statistical properties of the selected genes than in the Drosophila data. This suggests that methods developed in this challenge are able to extract generalizable properties of genes that are useful to accurately reconstruct the spatial arrangement of cells in tissues.

scholarly journals H3K9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis

2019 ◽  
Author(s):  
Andrey Poleshko ◽  
Cheryl L. Smith ◽  
Son C. Nguyen ◽  
Priya Sivaramakrishnan ◽  
John Isaac Murray ◽  
...  
Keyword(s):  
Cell Division ◽  
Spatial Organization ◽  
Nuclear Periphery ◽  
Nuclear Lamina ◽  
Positional Information ◽  
Specific Gene ◽  
Cell Type ◽  
Histone 3 ◽  
Spatial Positioning ◽  
Peripheral Heterochromatin

AbstractCell-type-specific 3D organization of the genome is unrecognizable during mitosis. It remains unclear how essential positional information is transmitted through cell division such that a daughter cell recapitulates the spatial genome organization of the parent. Lamina-associated domains (LADs) are regions of repressive heterochromatin positioned at the nuclear periphery that vary by cell type and contribute to cell-specific gene expression and identity. Here we show that histone 3 lysine 9 dimethylation (H3K9me2) is an evolutionarily conserved, specific mark of nuclear peripheral heterochromatin and that it is retained through mitosis. During mitosis, phosphorylation of histone 3 serine 10 temporarily shields the H3K9me2 mark allowing for dissociation of chromatin from the nuclear lamina. Using high-resolution 3D immuno-oligoFISH, we demonstrate that H3K9me2-enriched genomic regions, which are positioned at the nuclear lamina in interphase cells prior to mitosis, re-associate with the forming nuclear lamina before mitotic exit. The H3K9me2 modification of peripheral heterochromatin ensures that positional information is safeguarded through cell division such that individual LADs are re-established at the nuclear periphery in daughter nuclei. Thus, H3K9me2 acts as a 3D architectural mitotic guidepost. Our data establish a mechanism for epigenetic memory and inheritance of spatial organization of the genome.

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