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Methods in Molecular Biology (Clifton,... 2013RNA-seq or transcriptome analysis of individual cells and small-cell populations is essential for virtually any biomedical field. It is especially critical for...
RNA-seq or transcriptome analysis of individual cells and small-cell populations is essential for virtually any biomedical field. It is especially critical for developmental, aging, and cancer biology as well as neuroscience where the enormous heterogeneity of cells present a significant methodological and conceptual challenge. Here we present two methods that allow for fast and cost-efficient transcriptome sequencing from ultra-small amounts of tissue or even from individual cells using semiconductor sequencing technology (Ion Torrent, Life Technologies). The first method is a reduced representation sequencing which maximizes capture of RNAs and preserves transcripts' directionality. The second, a template-switch protocol, is designed for small mammalian neurons. Both protocols, from cell/tissue isolation to final sequence data, take up to 4 days. The efficiency of these protocols has been validated with single hippocampal neurons and various invertebrate tissues including individually identified neurons within a simpler memory-forming circuit of Aplysia californica and early (1-, 2-, 4-, 8-cells) embryonic and developmental stages from basal metazoans.
Topics: Aging; Animals; Aplysia; Base Sequence; Gene Expression Profiling; Genome; Hippocampus; Neurons; Sequence Analysis, RNA; Transcriptome
PubMed: 23929110
DOI: 10.1007/978-1-62703-556-9_18 -
Molecules (Basel, Switzerland) Feb 2020Invertebrates are an important source of structurally-diverse and biologically-active halogenated metabolites. The sea hare Rang has long been known to possess... (Review)
Review
Invertebrates are an important source of structurally-diverse and biologically-active halogenated metabolites. The sea hare Rang has long been known to possess halogenated metabolites of dietary origin that are used as a self-defense mechanism. The compounds from Rang are comprised mainly of terpenoids and small percentages of C-15 acetogenins, indoles, macrolides, sterols and alkaloids with potent cytotoxic, anti-microbial and anti-inflammatory properties. For decades the metabolites discovered have been investigated for their medical and pharmaceutical applications, so much so that the ecological role of the metabolites has been overlooked. The interaction between Rang and its diet that is comprised of seaweed can provide information into the distribution and diversity of the seaweed, the application of bioaccumulated secondary metabolites as part of its defense mechanism and the potential roles of these metabolites for adaptation in the marine environment. This paper compiles the diversity of halogenated secondary metabolites documented from Rang.
Topics: Acetogenins; Alkaloids; Animals; Aplysia; Halogenation; Indoles; Macrolides; Seaweed; Sterols
PubMed: 32070000
DOI: 10.3390/molecules25040815 -
Proceedings of the National Academy of... Sep 2021Habituation and sensitization (nonassociative learning) are among the most fundamental forms of learning and memory behavior present in organisms that enable adaptation...
Habituation and sensitization (nonassociative learning) are among the most fundamental forms of learning and memory behavior present in organisms that enable adaptation and learning in dynamic environments. Emulating such features of intelligence found in nature in the solid state can serve as inspiration for algorithmic simulations in artificial neural networks and potential use in neuromorphic computing. Here, we demonstrate nonassociative learning with a prototypical Mott insulator, nickel oxide (NiO), under a variety of external stimuli at and above room temperature. Similar to biological species such as , habituation and sensitization of NiO possess time-dependent plasticity relying on both strength and time interval between stimuli. A combination of experimental approaches and first-principles calculations reveals that such learning behavior of NiO results from dynamic modulation of its defect and electronic structure. An artificial neural network model inspired by such nonassociative learning is simulated to show advantages for an unsupervised clustering task in accuracy and reducing catastrophic interference, which could help mitigate the stability-plasticity dilemma. Mott insulators can therefore serve as building blocks to examine learning behavior noted in biology and inspire new learning algorithms for artificial intelligence.
Topics: Algorithms; Animals; Aplysia; Artificial Intelligence; Electrons; Insulator Elements; Models, Neurological; Neural Networks, Computer; Neuronal Plasticity; Nickel; Synapses
PubMed: 34531299
DOI: 10.1073/pnas.2017239118 -
Current Biology : CB Jan 2011
Topics: Animals; Aplysia; Genome; Memory; Neurons
PubMed: 21256433
DOI: 10.1016/j.cub.2010.11.028 -
Proceedings of the National Academy of... Jul 2022The gastropod mollusk is an important model for cellular and molecular neurobiological studies, particularly for investigations of molecular mechanisms of learning and...
The gastropod mollusk is an important model for cellular and molecular neurobiological studies, particularly for investigations of molecular mechanisms of learning and memory. We developed an optimized assembly pipeline to generate an improved nervous system transcriptome. This improved transcriptome enabled us to explore the evolution of cognitive capacity at the molecular level. Were there evolutionary expansions of neuronal genes between this relatively simple gastropod (20,000 neurons) and (500 million neurons), the invertebrate with the most elaborate neuronal circuitry and greatest behavioral complexity? Are the tremendous advances in cognitive power in vertebrates explained by expansion of the synaptic proteome that resulted from multiple rounds of whole genome duplication in this clade? Overall, the complement of genes linked to neuronal function is similar between and As expected, a number of synaptic scaffold proteins have more isoforms in humans than in or . However, several scaffold families present in mollusks and other protostomes are absent in vertebrates, including the Fifes, Lev10s, SOLs, and a NETO family. Thus, whereas vertebrates have more scaffold isoforms from select families, invertebrates have additional scaffold protein families not found in vertebrates. This analysis provides insights into the evolution of the synaptic proteome. Both synaptic proteins and synaptic plasticity evolved gradually, yet the last deuterostome-protostome common ancestor already possessed an elaborate suite of genes associated with synaptic function, and critical for synaptic plasticity.
Topics: Animals; Aplysia; Biological Evolution; Cognition; Neuronal Plasticity; Neurons; Protein Isoforms; Proteome; Synapses; Transcriptome
PubMed: 35867761
DOI: 10.1073/pnas.2122301119 -
BMC Genomics Jul 2022The immune repertoires of mollusks beyond commercially important organisms such as the pacific oyster Crassostrea gigas or vectors for human pathogens like the...
The immune repertoires of mollusks beyond commercially important organisms such as the pacific oyster Crassostrea gigas or vectors for human pathogens like the bloodfluke planorb Biomphalaria glabrata are understudied. Despite being an important model for neural aging and the role of inflammation in neuropathic pain, the immune repertoire of Aplysia californica is poorly understood. Recent discovery of a neurotropic nidovirus in Aplysia has highlighted the need for a better understanding of the Aplysia immunome. To address this gap in the literature, the Aplysia reference genome was mined using InterProScan and OrthoFinder for putative immune genes. The Aplysia genome encodes orthologs of all critical components of the classical Toll-like receptor (TLR) signaling pathway. The presence of many more TLRs and TLR associated adapters than known from vertebrates suggest yet uncharacterized, novel TLR associated signaling pathways. Aplysia also retains many nucleotide receptors and antiviral effectors known to play a key role in viral defense in vertebrates. However, the absence of key antiviral signaling adapters MAVS and STING in the Aplysia genome suggests divergence from vertebrates and bivalves in these pathways. The resulting immune gene set of this in silico study provides a basis for interpretation of future immune studies in this important model organism.
Topics: Animals; Aplysia; Biomphalaria; Crassostrea; Genome; Humans; Immunity, Innate; Signal Transduction
PubMed: 35906538
DOI: 10.1186/s12864-022-08780-6 -
Journal of Neuroscience Methods Apr 2022A growing body of research demonstrates that focused ultrasound stimulates activity in human and other mammalian nervous systems. However, there is no consensus on which...
BACKGROUND
A growing body of research demonstrates that focused ultrasound stimulates activity in human and other mammalian nervous systems. However, there is no consensus on which sonication parameters are optimal. Furthermore, the mechanism of action behind ultrasound neurostimulation remains poorly understood. An invertebrate model greatly reduces biological complexity, permitting a systematic evaluation of sonication parameters suitable for ultrasound neurostimulation.
NEW METHOD
Here, we describe the use of focused ultrasound stimulation with an ex-vivo abdominal ganglion preparation of the California sea hare, Aplysia californica, a long-standing model system in neurobiology. We developed a system for stimulating an isolated ganglion preparation while obtaining extracellular recordings from nerves. The focused ultrasound stimulation uses one of two single-element transducers, enabling stimulation at four distinct carrier frequencies (0.515 MHz, 1.l MHz, 1.61 MHz, 3.41 MHz).
RESULTS
Using continuous wave ultrasound, we stimulated the ganglion at all four frequencies, and we present quantitative evaluation of elicited activation at four different sonication durations and three peak pressure levels, eliciting up to a 57-fold increase in spiking frequency.
COMPARISON WITH ELECTRICAL STIMULATION
We demonstrated that ultrasound-induced activation is repeatable, and the response consistency is comparable to electrical stimulation.
CONCLUSIONS
Due to the relative ease of long-term recordings for many hours, this ex-vivo ganglion preparation is suitable for investigating sonication parameters and the effects of focused ultrasound stimulation on neurons.
Topics: Animals; Aplysia; Electric Stimulation; Humans; Mammals; Neurons; Transducers
PubMed: 35227740
DOI: 10.1016/j.jneumeth.2022.109536 -
Scientific Reports Jun 2021Electric currents can produce quick, reversible control of neural activity. Externally applied electric currents have been used in inhibiting certain ganglion cells in...
Electric currents can produce quick, reversible control of neural activity. Externally applied electric currents have been used in inhibiting certain ganglion cells in clinical practices. Via electromagnetic induction, a miniature-sized magnetic coil could provide focal stimulation to the ganglion neurons. Here we report that high-frequency stimulation with the miniature coil could reversibly block ganglion cell activity in marine mollusk Aplysia californica, regardless the firing frequency of the neurons, or concentration of potassium ions around the ganglion neurons. Presence of the ganglion sheath has minimal impact on the inhibitory effects of the coil. The inhibitory effect was local to the soma, and was sufficient in blocking the neuron's functional output. Biophysical modeling confirmed that the miniature coil induced a sufficient electric field in the vicinity of the targeted soma. Using a multi-compartment model of Aplysia ganglion neuron, we found that the high-frequency magnetic stimuli altered the ion channel dynamics that were essential for the sustained firing of action potentials in the soma. Results from this study produces several critical insights to further developing the miniature coil technology for neural control by targeting ganglion cells. The miniature coil provides an interesting neural modulation strategy in clinical applications and laboratory research.
Topics: Action Potentials; Animals; Aplysia; Ganglia, Invertebrate; Magnetic Fields; Neurons
PubMed: 34193906
DOI: 10.1038/s41598-021-93114-x -
Acta Biochimica Polonica 2003A distinction between short-term memories lasting minutes to hours and long-term memories lasting for many days is that the formation of long-term memories requires new... (Review)
Review
A distinction between short-term memories lasting minutes to hours and long-term memories lasting for many days is that the formation of long-term memories requires new gene expression. In this review, the focus is on the current understanding of the relation of transcription to memory consolidation based on the data collected from behavioral studies performed primarily on genetically altered animals. Studies in Drosophila and Aplysia indicate that the transcription factor cAMP/Ca(2+) response element binding protein (CREB) is critical in mediating the conversion from short- to long-term memory. More recent genetic studies in mice also demonstrated CREB and inducible transcription factor Zif268 involvement in information storage processes. Transcription seems to play essential role in memory formation but the mechanisms for activation of transcription and downstream processes during memory consolidation remain unclear.
Topics: Animals; Aplysia; Cyclic AMP Response Element-Binding Protein; Drosophila; Gene Expression Regulation; Memory; Memory, Short-Term; Mice; Transcription, Genetic
PubMed: 14515157
DOI: No ID Found -
Learning & Memory (Cold Spring Harbor,... 2023Neuropeptides are widely used as neurotransmitters in vertebrates and invertebrates. In vertebrates, a detailed understanding of their functions as transmitters has been...
Neuropeptides are widely used as neurotransmitters in vertebrates and invertebrates. In vertebrates, a detailed understanding of their functions as transmitters has been hampered by the complexity of the nervous system. The marine mollusk , with a simpler nervous system and many large, identified neurons, presents several advantages for addressing this question and has been used to examine the roles of tens of peptides in behavior. To screen for other peptides that might also play roles in behavior, we observed immunoreactivity in individual neurons in the central nervous system of adult with antisera raised against the peptide FMRFamide and two mammalian peptides that are also found in , cholecystokinin (CCK) and neuropeptide Y (NPY), as well as serotonin (5HT). In addition, we observed staining of individual neurons with antisera raised against mammalian somatostatin (SOM) and peptide histidine isoleucine (PHI). However, genomic analysis has shown that these two peptides are not expressed in the nervous system, and we have therefore labeled the unknown peptides stained by these two antibodies as X and X There was an area at the anterior end of the cerebral ganglion that had staining by antisera raised against many different transmitters, suggesting that this may be a modulatory region of the nervous system. There was also staining for X and, in some cases, FMRFamide in the bag cell cluster of the abdominal ganglion. In addition, these and other studies have revealed a fairly high degree of colocalization of different neuropeptides in individual neurons, suggesting that the peptides do not just act independently but can also interact in different combinations to produce complex functions. The simple nervous system of is advantageous for further testing these ideas.
Topics: Animals; Aplysia; FMRFamide; Central Nervous System; Neuropeptides; Ganglia; Mammals
PubMed: 37442624
DOI: 10.1101/lm.053758.123