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Comparison between WT and bes1 in an in vitro tissue culture system, VISUAL

ABSTRACT: Comparison between WT and bes1 in an in vitro tissue culture system, VISUAL

PROVIDER: PRJNA433158 | ENA |

REPOSITORIES: ENA

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Comparison between WT and bes1 in an in vitro tissue culture system, VISUAL

Project description:We have previously established an in vitro tissue culture system (named VISUAL; Kondo et al., 2016), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons To compare gene expression profiles between WT and bes1 during vascular development, we performed GeneChip analysis using VISUAL.

2018-02-07 | GSE110199 | GEO

Comparison between WT and apl in a novel in vitro tissue culture system, VISUAL

Project description:We established a novel in vitro tissue culture system (named VISUAL), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons To compare gene expression profiles between WT and apl during vascular development, we performed GeneChip analysis using VISUAL.

2016-05-25 | GSE80026 | GEO

Comparison among samples subjected to a novel in vitro tissue culture system, VISUAL-CC

Project description:We established a novel in vitro tissue culture system (named VISUAL-CC), in which phloem companion cell (CC) differentiation can be induced with Arabidopsis thaliana cotyledons. To compare gene expression profiles between VISUAL and VISUAL-CC, we conducted GeneChip analysis using two different in vitro cultures. CC-S means a sample that strongly induces CC differentiation. CC-M means a sample that moderately induces CC differentiation. V means a VISUAL sample, that does not induce CC differentiation at all.

2020-03-31 | GSE141037 | GEO

Cell-sorting analysis with SEOR1pro::SEOR1-YFP in a novel in vitro tissue culture system, VISUAL

Project description:We established a novel in vitro tissue culture system (named VISUAL), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons To isolate phloem-specific genes in VISUAL, we performed GeneChip analysis after cell-sorting experiments with SEOR1pro::SEOR1-YFP.

2016-05-25 | GSE80027 | GEO

Comparison among samples subjected to a novel in vitro tissue culture system, VISUAL-CC

Project description:Comparison among samples subjected to a novel in vitro tissue culture system, VISUAL-CC

| PRJNA591818 | ENA

The effects of different types of sugars on vascular cell diffentiation in a tissue culture system, VISUAL

Project description:We established a novel in vitro tissue culture system (named VISUAL), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons To investigate the effects of differenet sugars in VISUAL, we performed GeneChip analysis .

2023-05-16 | GSE223284 | GEO

Six-hour interval time-course expression data during VISUAL

Project description:We used in vitro tissue culture system (named VISUAL), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons To investigate temporal gene expression profiles during ectopic vascular cell defferentiaction processes, we performed GeneChip analysis using VISUAL.

2021-05-19 | GSE171548 | GEO

Cell types and molecular architecture of the Octopus bimaculoides visual system

Project description:Cephalopods have a remarkable visual system, with a camera-type eye, high acuity vision, and a wide range of sophisticated visual behaviors. However, the cephalopod brain is organized dramatically differently from that of vertebrates, as well as other invertebrates, and little is known regarding the cell types and molecular determinants of their visual system organization beyond neuroanatomical descriptions. Here we present a comprehensive single-cell molecular atlas of the octopus optic lobe, which is the primary visual processing structure in the cephalopod brain. We combined single-cell RNA sequencing with RNA fluorescence in situ hybridization to both identify putative molecular cell types and determine their anatomical and spatial organization within the optic lobe. Our results reveal six major neuronal cell classes identified by neurotransmitter/neuropeptide usage, in addition to non-neuronal and immature neuronal populations. Moreover, we find that additional markers divide these neuronal classes into subtypes with distinct anatomical localizations, revealing cell type diversity and a detailed laminar organization within the optic lobe. We also delineate the immature neurons within this continuously growing tissue into subtypes defined by evolutionarily conserved fate specification genes as well as novel cephalopod- and octopus- specific genes. Together, these findings outline the organizational logic of the octopus visual system, based on functional determinants, laminar identity, and developmental markers/pathways. The resulting atlas presented here delineates the “parts list” of the neural circuits used for vision in octopus, providing a platform for investigations into the development and function of the octopus visual system as well as the evolution of visual processing.

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Analysis of experience-regulated transcriptome and imprintome during critical periods of mouse visual system development

Project description:Visual system development is light-experience dependent, which strongly implicates epigenetic mechanisms in light-regulated maturation. Among many epigenetic processes, genomic imprinting is an epigenetic mechanism through which monoallelic gene expression occurs in a parent-of-origin-specific manner. It is unknown if genomic imprinting contributes to visual system development. We profiled the transcriptome and imprintome during critical periods of mouse visual system development under normal- and dark-rearing conditions using B6/CAST F1 hybrid mice. We identified experience-regulated, isoform-specific, and brain region-specific imprinted genes. We also found imprinted microRNAs were predominantly clustered into the Dlk1-Dio3 imprinted locus with light experience affecting some imprinted miRNA expression. Our findings provide the first comprehensive analysis of light-experience regulation of the transcriptome and imprintome during critical periods of visual system development. Our results may contribute to therapeutic strategies for visual impairments and circadian rhythm disorders resulting from a dysfunctional imprintome.

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Proteomic screen reveals diverse protein transport between connected neurons in the visual system.

Project description:Intercellular transfer of toxic proteins between neurons is thought to contribute to neurodegenerative disease, however whether direct inter-neuronal protein transfer occurs in the healthy brain is not clear. To assess the prevalence and identity of transferred proteins and the cellular specificity of transfer, we biotinylated retinal ganglion cell proteins in vivo and examined biotinylated proteins transported through the rodent visual circuit using microscopy, biochemistry, and mass spectrometry. Electron microscopy demonstrated preferential transfer of biotinylated proteins from retinogeniculate inputs to excitatory LGN neurons compared to GABAergic neurons. An unbiased mass spectrometry-based screen identified 200 transneuronally transported proteins (TNTPs) isolated from visual cortex. The majority of TNTPs are present in neuronal exosomes and virally-expressed TNTPs, including tau and beta-synuclein, were detected in isolated exosomes and postsynaptic neurons. Our data demonstrate transfer of diverse endogenous proteins between neurons in the healthy intact brain and suggest that TNTP transport may be mediated by exosomes.

2022-01-10 | MSV000088669 | MassIVE

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