Aplysia kinesin mRNA cargo study
Ontology highlight
ABSTRACT:
ORGANISM(S): Aplysia californica
SUBMITTER: Sergey Kalachikov
PROVIDER: E-GEOD-30389 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
A strategy to capture and characterize the synaptic transcriptome.
Puthanveettil Sathyanarayanan V SV Antonov Igor I Kalachikov Sergey S Rajasethupathy Priyamvada P Choi Yun-Beom YB Kohn Andrea B AB Citarella Mathew M Yu Fahong F Karl Kevin A KA Kinet Maxime M Morozova Irina I Russo James J JJ Ju Jingyue J Moroz Leonid L LL Kandel Eric R ER
Proceedings of the National Academy of Sciences of the United States of America 20130415 18
Here we describe a strategy designed to identify RNAs that are actively transported to synapses during learning. Our approach is based on the characterization of RNA transport complexes carried by molecular motor kinesin. Using this strategy in Aplysia, we have identified 5,657 unique sequences consisting of both coding and noncoding RNAs from the CNS. Several of these RNAs have key roles in the maintenance of synaptic function and growth. One of these RNAs, myosin heavy chain, is critical in pr ...[more]
Similar Datasets
Project description:Whole genome transcriptional profiling is used to compare ESTs found in cell bodies and processes of Aplysia motor neurons RNA samples derived from cell bodies or processes of Aplysia single cultured motor neurons were hybridized to custom Aplysia EST microarrays. Two-condition experiment; four biological replicates for each condition were reciprocally hybridized on each two-color array
2013-04-26 | E-GEOD-30387 | biostudies-arrayexpress
Project description:Whole genome transcriptional profiling is used to compare ESTs found in cell bodies and processes of Aplysia sensory neurons RNA samples derived from cell bodies or processes of Aplysia single cultured sensory neurons were hybridized to custom Aplysia EST microarrays. Two-condition experiment; four biological replicates for each condition were reciprocally hybridized on each two-color array
2013-04-26 | E-GEOD-30388 | biostudies-arrayexpress
Project description:Specific mRNAs are transported from the cell body to synapses where their translation can modify communication of pre-existing synapses and induce formation of new synaptic connections in response to learning. Little is known, however, about the identity of the RNAs that are actively transported and when and how these RNAs are utilized during learning. By focusing on RNAs that are associated with kinesin, a motor protein that transports gene products from the cell body to synapses, we have now applied microarrays and 454 sequencing to identify actively transported RNAs from the Aplysia central nervous system. Using a library prepared from the kinesin complex immunoprecipitated from the central nervous system (CNS), we have identified thousands of unique transcripts, of which ~600 mRNAs were annotated. Two sample comparison: kinesin IP vs. control.
2013-04-24 | E-GEOD-30440 | biostudies-arrayexpress
Project description:The complexity of events associated with age-related memory loss (ARML) cannot be overestimated. The problem is further complicated by the enormous diversity of neurons in the CNS and even synapses of one neuron within a neural circuit. Large-scale single-neuron analysis is not only challenging but mostly impractical for any model currently used in ARML. We simply do not know: do all neurons and synapses age differently or are some neurons (or synapses) more resistant to aging than others? What is happening in any given neuron while it undergoes “normal” aging? What are the genomic changes that make aging apparently irreversible? What would be the balance between neuron-specific vs global genome-wide changes in aging? In the proposed paper we address these questions and develop a new model to study the entire scope of genomic and epigenomic regulation in aging at the resolution of single functionally characterized cells and even cell compartments. In particular, the mollusc Aplysia californica has been implemented as a powerful paradigm in addressing fundamental questions of the neurobiology of aging. The proposed manuscript will consist of four parts. First, we will provide an introduction to Aplysia as a representative of the largest superclade of bilaterian animals (Lophotrochozoa). Aplysia has a short lifespan of 220-300 days with a well-characterized life cycle and characterized phenomenology of aging. Most importantly, Aplysia possess the largest nerve cells in the entire animal kingdom (only eggs are larger); these cells can be uniquely identified and mapped in terms of their well-defined interactions with other neurons forming relatively simpler neural circuits underlying several stereotypic and learned behaviors. Second, we have identified in Aplysia more that a hundred neurological- and age-related genes that were lost in other established invertebrate models (such as Drosophila and C. elegans). The proposed long-term regulatory age-related mechanisms include a high level of conservation among many epigenetic processes known to be lost in nematodes and flies with extremely short lifecycles and particularly derived genomes. We also identify and cloned more than 30 evolutionarily conserved homologs of genes involved in Alzheimer’s, Parkinson’s and Huntington’s diseases as well as age-related hormones. Third, we performed genome-wide analysis of expression patterns of more than 55,000 unique transcripts by comparing two different identified cholinergic neurons (R2 and LPl1) among young and aged animals. This direct single neuron genomic analysis indicates that there are significant cell-specific changes in gene-expression profiles as a function of aging. We estimated that only ~10-20% of genes that are differently expressed in the aging brain are common for all neuronal types - the remaining 80% are neuron-specific (i.e. found in aging neurons of one but not another type). The list of “common aging genes” includes components of insulin growth factor pathways, cell bioenergetics, telomerase-associated proteins, antioxidant enzymes, water channels and estrogen receptors. The rest were neuron-specific gene products (including apoptosis-related proteins, Alzheimer-related genes, growth factors and their receptors, ionic channels, transcription factors and more than 120 identified proteins known to be involved in neurodevelopment and synaptogenesis). Surprisingly, even two different identified cholinergic motoneurons age differently and each of them has a unique subset of genes differentially expressed in older animals. Fourth, we showed that the activity of the entire genome and associated epigenomic modifications (e.g. DNA methylation, histone dynamics) can be efficiently monitored within a single Aplysia neuron and can be modified as a function of aging in a neuron-specific manner including selective histones and histone-modifying enzymes and DNA methylation-related enzymes. This genome-wide analysis of aging allows us to propose novel mechanisms of active DNA demethylation and cell-specific methylation as well as regional relocation of RNAs as three key processes underlying age-related memory loss. These mechanisms tune the dynamics of long-term chromatin remodeling, control weakening and the loss of synaptic connections in aging. At the same time, our genomic tests revealed evolutionarily conserved gene clusters in the Aplysia genome associated with senescence and regeneration (e.g. apoptosis- and redox- dependent processes, insulin signaling, etc.). This is a reference design experiment with all samples being compared to one CNS from Aplysia. Two cholinergic neurons (R2 and LPl1), two ages (young and old), two arrays (AAA and DAA), three biological replicates each sample type. Two direct comparison experiments were also performed. One with young and old abdominal ganglion and the other with young and old R2.
2010-05-20 | E-GEOD-18783 | biostudies-arrayexpress
Project description:Whole genome transcriptional profiling is used to identify ESTs found in RNA co-immunoprecipitated from Aplysia CNS with antibodies against Aplysia Kinesin Heavy Chain (ApKHC) RNA derived from Aplysia CNS served as control in the opposite channel. Custom Aplysia EST array to probe the samples was designed and ordered from Agilent. Two-condition experiment; four biological replicates for each condition were reciprocally hybridized on each two-color array
2013-04-26 | E-GEOD-30386 | biostudies-arrayexpress
Project description:Understanding evolutionary mechanisms underlying expansion and reorganization of the human brain represents an important aspect in analyzing the emergence of cognitive abilities typical of our species. Comparative analyses of neuronal phenotypes in closest living relatives (Pan troglodytes; the common chimpanzee) can shed the light into changes in neuronal morphology compared to the last common ancestor (LCA), opening possibilities for analyses of the timing of their appearance, and the role of evolutionary mechanisms favoring a particular type of information processing in humans. Here, we use induced pluripotent stem cell (iPSC) technology to model neural progenitor cell migration and early development of cortical pyramidal neurons in humans and chimpanzees. In addition, we provide morphological characterization of the early stages of neuronal development in human and chimpanzee transplanted cells, and examine the role of developmental mechanisms previously proposed for the evolutionary expansions of the human brain on the early development of pyramidal neurons in the two species. The strategy proposed here lay down the basis for further comparative analysis between human and non-human primates and opens new avenues for understanding cognitive capability and neurological disease susceptibility differences between species. PolyA RNA-Seq profiling of neural progenitor cells (NPCs) and neurons differentiated from human and chimpanzee iPSCs.
2016-08-07 | E-GEOD-83638 | biostudies-arrayexpress
Project description:Despite the advances in our understanding of aging-associated behavioral decline, we know relatively little about how aging affect neural circuits that underlie specific behaviors. Specifically, we know little about how aging affect expression of genes in specific neural circuits. We have now addressed this problem by exploring a cholinergic neuron R15, an identified neuron of marine snail Aplysia. R15 is characterized by bursting action potentials and is implicated in reproduction, osmoregulation and locomotion. We examined changes in gene expression in R15 neurons during aging by microarray analyses of RNAs prepared from two different age groups, mature and old animals. Specifically we find that 1083 ESTs are differentially regulated in mature and old R15 neurons. Bioinformatics analyses of these genes have identified specific biological pathways and molecular processes that are up or down regulated in mature and old neurons. Comparison with human signaling networks using pathway analyses have identified three major networks that are altered in old R15 neurons. Furthermore, by single neuron qRTPCR we examined expression levels of candidate regulators involved in transcription (CREB1) and translation (S6 kinase) and find that aging is associated with a decrease in expression of these regulators. We next studied expression of CREB1 and S6 kinase in two different motor neurons (L7 and L11) and another cholinergic neuron R2 and find that these neurons have characteristic changes in gene expression during aging
2014-02-05 | E-GEOD-46618 | biostudies-arrayexpress
Project description:These arrays were conducted in order to confirm the generation of astrocytes from human embryonic stem cells and to determine expression differences between astrocyte subtypes. Experiment Overall Design: Human embryonic stem cells were differentated in vitro to neuroepithelial cells (day-17), neurons (day-50), or astrocytes (day-180) after specification with the morphogens retinoic acid (RA) or FGF8 from days 10-21.
2009-11-28 | E-GEOD-18959 | biostudies-arrayexpress
Project description:We used a custom-designed microarray and qPCR to characterize the rapid transcriptional response to long-term sensitization training in the marine mollusk Aplysia californica. Aplysia were exposed to repeated noxious shocks to one side of the body (4 ten-second shocks at 90mA, 30 min ISI), a procedure known to induce a transcription-dependent and long-lasting increase in reflex responsiveness that is restricted to the side of training. One hour after training, pleural ganglia from the trained and untrained sides of the body were harvested; these ganglia contain the sensory nociceptors which help mediate the expression of long-term sensitization memory. Â Microarray analysis from 8 biological replicates suggests that long-term sensitization training rapidly regulates at least 102 transcripts. We used qPCR to test a subset of these transcripts and found that 86% were confirmed in the same samples, and 83% of these were again confirmed in an independent sample (n = 9 animals). Thus, our new microarray design shows very strong convergent and predictive validity for analyzing the transcriptional correlates of memory in Aplysia. Fully validated transcripts include some previously identified as regulated in this paradigm (ApC/EBP and ApEgr) but also include novel findings. Specifically, we show that long-term sensitization training rapidly up-regulates the expression of transcripts which encode a C/EBP gamma, a glycine transporter, and a vacuolar-protein-sorting-associated protein. Within-subjects comparison of trained (Cy5) to untrained (Cy3) pleural ganglia with 8 biological replicates. Each replicate is a trained sample from two animals (right and left trained) and each untrained sample is from the same two aniamls (right and left untrained)
2014-05-08 | E-GEOD-57458 | biostudies-arrayexpress
Project description:Primary cortical neurons were isolated from E15 mice and after 5 days in vitro were untreated or treated for 24 h with mesenchymal stem cell conditioned medium and then untreated or treated for a further 24 h with NMDA. Neuron gene expression was profiled and compared between the four different conditions (neurons, neurons+MSC cm, neurons+NMDA, neurons+MSC cm+NMDA) to investigate the molecular mechanisms of MSC neuroprotection. Mesenchymal stem cells (MSC) promote functional recovery in experimental models of central nervous system (CNS) pathology and are currently being tested in clinical trials for stroke, multiple sclerosis and CNS injury. Their beneficial effects are attributed to activation of endogenous CNS repair processes and immune regulation but their mechanisms of action are poorly understood. Here we investigated the neuroprotective effects of MSC in simplified MSC-neuron co-culture systems and in mice using models of glutamate excitotoxicity. MSC protected primary cortical neurons against glutamate (NMDA) receptor-induced death and conditioned medium from MSC (MSC cm), but not control NIH3T3 cells, was sufficient for this effect. MSC cm neuroprotection in mouse cortical neurons was reduced by neutralizing antibodies to bFGF and associated with altered gene expression in neurons towards an immature phenotype as well as reduced neuronal Grin1, Grin2a and Grin2b mRNA levels in response to NMDA stimulation. Further, MSC cm neuroprotection in rat retinal ganglion cells was associated with absence of glutamate-induced calcium influx. Adoptive transfer of EGFP+MSC in a mouse kainic acid seizure model reduced CA3 neuron damage and hippocampal astrocytosis and resulted in the increased expression of neuronal genes that are upregulated by MSC cm, Bmi1, Ddx4, Ezh1, in the hippocampus. These results show that MSC mediate direct neuroprotection against glutamate excitotoxicity by secreting bFGF, reducing glutamate receptor expression and function and altering neuron gene expression towards an immature pattern, and provide evidence for a link between the therapeutic effects of MSC and the activation of endogenous repair processes following CNS injury. In vitro cultures primary cortical neurons from mice were protected from glutamate excitotoxicity when pre-treated with MSC cm. Global gene expression changes induced in neurons before and after treatment with MSC cm and/or NMDA were investigated using a cDNA spotted macroarray filter. Four samples were analysed in duplicate: neurons alone (untreated), neurons+MSC cm, neurons+NMDA, neurons+MSC cm+NMDA.
2011-05-01 | E-GEOD-26279 | biostudies-arrayexpress