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1.  A Prion-mediated Mechanism for Memory Proposed in Drosophila 
Neuron  2012;76(2):260-262.
Memories are remarkably persistent, but rely on transient signaling. The prion-like properties of CPEB suggested a solution to this problem. The paper by Krüttner et al demonstrates that the prion-like domain of Drosophila CPEB functions independently of its RNA binding domain for memory.
doi:10.1016/j.neuron.2012.10.001
PMCID: PMC3488862  PMID: 23083729
2.  microRNA-276a Functions in Ellipsoid Body and Mushroom Body Neurons for Naïve and Conditioned Olfactory Avoidance in Drosophila 
microRNA-mediated gene regulation plays a key role in brain development and function. But there are few cases in which the roles of individual miRNAs have been elucidated in behaving animals. We report a miR-276a::DopR regulatory module in Drosophila that functions in distinct circuits for naïve odor responses and conditioned odor memory. Drosophila olfactory aversive memory involves convergence of the odors (conditioned stimulus, CS) and the electric shock (unconditioned stimulus, US) in mushroom body (MB) neurons. Dopamine receptor, DopR, mediates the US inputs onto MB. Distinct dopaminergic neurons also innervate ellipsoid body (EB), where DopR function modulates arousal to external stimuli. We demonstrate that miR-276a is required in MB neurons for memory formation and in EB for naïve responses to odors. Both roles of miR-276a are mediated by tuning DopR expression. The dual role of this miR-276a::DopR genetic module in these two neural circuits highlights the importance of miRNA-mediated gene regulation within distinct circuits underlying both naïve behavioral responses and memory.
doi:10.1523/JNEUROSCI.4004-12.2013
PMCID: PMC3640307  PMID: 23536094
3.  Transposable Elements in TDP-43-Mediated Neurodegenerative Disorders 
PLoS ONE  2012;7(9):e44099.
Elevated expression of specific transposable elements (TEs) has been observed in several neurodegenerative disorders. TEs also can be active during normal neurogenesis. By mining a series of deep sequencing datasets of protein-RNA interactions and of gene expression profiles, we uncovered extensive binding of TE transcripts to TDP-43, an RNA-binding protein central to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Second, we find that association between TDP-43 and many of its TE targets is reduced in FTLD patients. Third, we discovered that a large fraction of the TEs to which TDP-43 binds become de-repressed in mouse TDP-43 disease models. We propose the hypothesis that TE mis-regulation contributes to TDP-43 related neurodegenerative diseases.
doi:10.1371/journal.pone.0044099
PMCID: PMC3434193  PMID: 22957047
4.  Genetic disruptions of Drosophila Pavlovian learning leave extinction learning intact 
Genes, brain, and behavior  2009;9(2):203-212.
Individuals that experience traumatic events may develop persistent post-traumatic stress disorder (PTSD). Patients with this disorder are commonly treated with exposure therapy, which has had limited long-term success. In experimental neurobiology, fear extinction is a model for exposure therapy. In this behavioral paradigm, animals are repeatedly exposed in a safe environment to the fearful stimulus, which leads to greatly reduced fear. Studying animal models of extinction already has lead to better therapeutic strategies and development of new candidate drugs. Lack of a powerful genetic model of extinction, however, has limited progress in identifying underlying molecular and genetic factors. In this study, we established a robust behavioral paradigm to study the short term effect (acquisition) of extinction in Drosophila melanogaster. We focused on the extinction of olfactory aversive one-day memory with a task that has been the main workhorse for genetics of memory in flies. Using this paradigm, we demonstrate that extinction can inhibit each of two genetically distinct forms of consolidated memory. We then used a series of single-gene mutants with known impact on associative learning, to examine effects on extinction. We find that extinction is intact in each of these mutants, suggesting that extinction learning relies on different molecular mechanisms than does Pavlovian learning.
doi:10.1111/j.1601-183X.2009.00548.x
PMCID: PMC2866079  PMID: 20015341
5.  Deconstructing Memory in Drosophila 
Current biology : CB  2005;15(17):R700-R713.
Unlike most organ systems, which have evolved to maintain homeostasis, the brain has been selected to sense and adapt to environmental stimuli by constantly altering interactions in a gene network that functions within a larger neural network. This unique feature of the central nervous system provides a remarkable plasticity of behavior, but also makes experimental investigations challenging. Each experimental intervention ramifies through both gene and neural networks, resulting in unpredicted and sometimes confusing phenotypic adaptations. Experimental dissection of mechanisms underlying behavioral plasticity ultimately must accomplish an integration across many levels of biological organization, including genetic pathways acting within individual neurons, neural network interactions which feed back to gene function, and phenotypic observations at the behavioral level. This dissection will be more easily accomplished for model systems such as Drosophila, which, compared with mammals, have relatively simple and manipulable nervous systems and genomes. The evolutionary conservation of behavioral phenotype and the underlying gene function ensures that much of what we learn in such model systems will be relevant to human cognition. In this essay, we have not attempted to review the entire Drosophila memory field. Instead, we have tried to discuss particular findings that provide some level of intellectual synthesis across three levels of biological organization: behavior, neural circuitry and biochemical pathways. We have attempted to use this integrative approach to evaluate distinct mechanistic hypotheses, and to propose critical experiments that will advance this field.
doi:10.1016/j.cub.2005.08.024
PMCID: PMC3044934  PMID: 16139203
6.  Ethanol Sensitivity and Tolerance in Long-Term Memory Mutants of Drosophila melanogaster 
Background
It has become increasingly clear that molecular and neural mechanisms underlying learning and memory and drug addiction are largely shared. To confirm and extend these findings, we analyzed ethanol-responsive behaviors of a collection of Drosophila long-term memory mutants.
Methods
For each mutant, sensitivity to the acute uncoordinating effects of ethanol was quantified using the inebriometer. Additionally, 2 distinct forms of ethanol tolerance were measured: rapid tolerance, which develops in response to a single brief exposure to a high concentration of ethanol vapor; and chronic tolerance, which develops following a sustained low-level exposure.
Results
Several mutants were identified with altered sensitivity, rapid or chronic tolerance, while a number of mutants exhibited multiple defects.
Conclusions
The corresponding genes in these mutants represent areas of potential overlap between learning and memory and behavioral responses to alcohol. These genes also define components shared between different ethanol behavioral responses.
doi:10.1111/j.1530-0277.2008.00659.x
PMCID: PMC3044939  PMID: 18435628
Alcohol; Sensitivity; Tolerance; Drosophila; Learning/Memory
7.  Short and Long-term memory in Drosophila require cAMP signaling in distinct neuron types 
Current biology : CB  2009;19(16):1341-1350.
Summary
Background
A common feature of memory and its underlying synaptic plasticity is that each can be dissected into short-lived forms involving modification or trafficking of existing proteins and long-term forms that require new gene expression. An underlying assumption of this cellular view of memory consolidation is that these different mechanisms occur within a single neuron. At the neuro-anatomical level, however, different temporal stages of memory can engage distinct neural circuits, a notion that has not been conceptually integrated with the cellular view.
Results
We have investigated this issue in the context of aversive Pavlovian olfactory memory in Drosophila. Previous studies have demonstrated a central role for cAMP signaling in the mushroom body (MB). The Ca++ responsive adenylyl cyclase rutabaga is believed to be a coincidence detector in γ neurons, one of the three principle classes of MB Kenyon cells. We are able to separately restore short-term or long-term memory to a rutabaga mutant with expression of rutabaga in different subsets of MB neurons.
Conclusions
Our findings suggest a model in which the learning experience initiates two parallel associations: a short-lived trace in MB γ neurons, and a long-lived trace in α/β neurons.
doi:10.1016/j.cub.2009.07.016
PMCID: PMC2752374  PMID: 19646879
8.  Parallel processing of olfactory memories in Drosophila 
Fly  2010;4(2):163-166.
One of the hallmarks of both memory and the underlying synaptic plasticity is that they each rely on short-lived and longer-lived forms. Short-lived memory is thought to rely on modification to existing proteins, whereas long-term memory requires induction of new gene expression. The most common view is that these two processes rely on signaling mechanisms within the same neurons. We recently demonstrated a dissection of the signaling requirements for short and long-lived memory into distinct sets of neurons. Using an aversive olfactory conditioning task in Drosophila, we found that cAMP signaling in different neuron cell types is sufficient to support short or long-term memory independently.
PMCID: PMC2888992  PMID: 20224292
9.  Identification of Synaptic Targets of Drosophila Pumilio 
PLoS Computational Biology  2008;4(2):e1000026.
Drosophila Pumilio (Pum) protein is a translational regulator involved in embryonic patterning and germline development. Recent findings demonstrate that Pum also plays an important role in the nervous system, both at the neuromuscular junction (NMJ) and in long-term memory formation. In neurons, Pum appears to play a role in homeostatic control of excitability via down regulation of para, a voltage gated sodium channel, and may more generally modulate local protein synthesis in neurons via translational repression of eIF-4E. Aside from these, the biologically relevant targets of Pum in the nervous system remain largely unknown. We hypothesized that Pum might play a role in regulating the local translation underlying synapse-specific modifications during memory formation. To identify relevant translational targets, we used an informatics approach to predict Pum targets among mRNAs whose products have synaptic localization. We then used both in vitro binding and two in vivo assays to functionally confirm the fidelity of this informatics screening method. We find that Pum strongly and specifically binds to RNA sequences in the 3′UTR of four of the predicted target genes, demonstrating the validity of our method. We then demonstrate that one of these predicted target sequences, in the 3′UTR of discs large (dlg1), the Drosophila PSD95 ortholog, can functionally substitute for a canonical NRE (Nanos response element) in vivo in a heterologous functional assay. Finally, we show that the endogenous dlg1 mRNA can be regulated by Pumilio in a neuronal context, the adult mushroom bodies (MB), which is an anatomical site of memory storage.
Author Summary
The Drosophila Pumilio (Pum) protein was originally identified as a translational control factor for embryo patterning. Subsequent studies have identified Pum's role in multiple biological processes, including the maintenance of germline stem cell, the proliferation and migration of primordial germ cells, olfactory leaning and memory, and synaptic plasticity. Pum is highly conserved across phyla, i.e., from worm to human; however, the mRNA targets of Pum within each tissue and organism are largely unknown. On the other hand, the prediction of RNA binding sites remains a hard question in the computational field. We were interested in finding Pum targets in the nervous system using fruit flies as a model organism. To accomplish this, we used the few Pum binding sequences that had previously been shown in vivo as “training sequences” to construct bioinformatic models of the Pum binding site. We then predicted a few Pum mRNA targets among the genes known to function in neuronal synapses. We then used a combination of “golden standards” to verify these predictions: a biochemical assay called gel shifts, and in vivo functional assays both in embryo and neurons. With these approaches, we successfully confirmed one of the targets as Dlg, which is the Drosophila ortholog of human PSD95. Therefore, we present a complete story from computational study to real biological functions.
doi:10.1371/journal.pcbi.1000026
PMCID: PMC2265480  PMID: 18463699

Results 1-9 (9)