@article {1092606,
	title = {Analysis of axonal trafficking via a novel live-imaging technique reveals distinct hedgehog transport kinetics},
	journal = {Biol Open},
	volume = {6},
	number = {5},
	year = {2017},
	month = {2017 May 15},
	pages = {714-721},
	abstract = {The Drosophila melanogaster (Dmel) eye is an ideal model to study development, intracellular signaling, behavior, and neurodegenerative disease. Interestingly, dynamic data are not commonly employed to investigate eye-specific disease models. Using axonal transport of the morphogen Hedgehog (Hh), which is integral to Dmel eye-brain development and implicated in stem cell maintenance and neoplastic disease, we demonstrate the ability to comprehensively quantify and characterize its trafficking in various neuron types and a neurodegeneration model in live early third-instar larval Drosophila We find that neuronal Hh, whose kinetics have not been reported previously, favors fast anterograde transport and varies in speed and flux with respect to axonal position. This suggests distinct trafficking pathways along the axon. Lastly, we report abnormal transport of Hh in an accepted model of photoreceptor neurodegeneration. As a technical complement to existing eye-specific disease models, we demonstrate the ability to directly visualize transport in real time in intact and live animals and track secreted cargoes from the axon to their release points. Particle dynamics can now be precisely calculated and we posit that this method could be conveniently applied to characterizing disease pathogenesis and genetic screening in other established models of neurodegeneration.},
	doi = {10.1242/bio.024075},
	author = {Daniele, Joseph R and Baqri, Rehan M and Kunes, Sam}
}
@article {1092611,
	title = {A novel proteolytic event controls Hedgehog intracellular sorting and distribution to receptive fields},
	journal = {Biol Open},
	volume = {6},
	number = {5},
	year = {2017},
	month = {2017 May 15},
	pages = {540-550},
	abstract = {The patterning activity of a morphogen depends on secretion and dispersal mechanisms that shape its distribution to the cells of a receptive field. In the case of the protein Hedgehog (Hh), these mechanisms of secretion and transmission remain unclear. In the developing Drosophila visual system, Hh is partitioned for release at opposite poles of photoreceptor neurons. Release into the retina regulates the progression of eye development; axon transport and release at axon termini trigger the development of postsynaptic neurons in the brain. Here we show that this binary targeting decision is controlled by a C-terminal proteolysis. Hh with an intact C-terminus undergoes axonal transport, whereas a C-terminal proteolysis enables Hh to remain in the retina, creating a balance between eye and brain development. Thus, we define a novel mechanism for the apical/basal targeting of this developmentally important protein and posit that similar post-translational regulation could underlie the polarity of related ligands.},
	doi = {10.1242/bio.024083},
	author = {Daniele, Joseph R and Chu, Tehyen and Kunes, Sam}
}
@article {662766,
	title = {Mitochondrial chaperone TRAP1 activates the mitochondrial UPR and extends healthspan in Drosophila.},
	journal = {Mech Ageing Dev},
	volume = {141-142},
	year = {2014},
	month = {2014 Nov-Dec},
	pages = {35-45},
	abstract = {The molecular mechanisms influencing healthspan are unclear but mitochondrial function, resistance to oxidative stress and proteostasis are recurring themes. Tumor necrosis factor Receptor Associated Protein 1 (TRAP1), the mitochondrial analog of Hsp75, regulates levels of reactive oxygen species in vitro and is found expressed at higher levels in tumor cells where it is thought to play a pro-survival role. While TRAP1-directed compartmentalized protein folding is a promising target for cancer therapy, its role at the organismal level is unclear. Here we report that overexpression of TRAP1 in Drosophila extends healthspan by enhancing stress resistance, locomotor activity and fertility while depletion of TRAP1 has the opposite effect, with little effect on lifespan under both conditions. In addition, modulating TRAP1 expression promotes the nuclear translocation of homeobox protein Dve and increases expression of genes associated with the mitochondrial unfolded protein response (UPR(mt)), indicating an activation of this proteostasis pathway. Notably, independent genetic knockdown of components of the UPR(mt) pathway dampen the enhanced stress resistance observed in TRAP1 overexpression flies. Together these studies suggest that TRAP1 regulates healthspan, potentially through activation of the UPR(mt).},
	keywords = {Animals, Drosophila melanogaster, Drosophila Proteins, HSP90 Heat-Shock Proteins, Longevity, Mitochondria, Mitochondrial Proteins, Unfolded Protein Response},
	issn = {1872-6216},
	doi = {10.1016/j.mad.2014.09.002},
	author = {Baqri, Rehan M and Pietron, Arielle V and Gokhale, Rewatee H and Turner, Brittany A and Kaguni, Laurie S and Shingleton, Alexander W and Kunes, Sam and Miller, Kyle E}
}
@article {662776,
	title = {Determinants of the Drosophila odorant receptor pattern.},
	journal = {Dev Cell},
	volume = {22},
	number = {2},
	year = {2012},
	month = {2012 Feb 14},
	pages = {363-76},
	abstract = {In most olfactory systems studied to date, neurons that express the same odorant receptor (Or) gene are scattered across sensory epithelia, intermingled with neurons that express different Or genes. In Drosophila, olfactory sensilla that express the same Or gene are dispersed on the antenna and the maxillary palp. Here we show that Or identity is specified in a spatially stereotyped pattern by the cell-autonomous activity of the transcriptional regulators Engrailed and Dachshund. Olfactory sensilla then become highly motile and disperse beneath the epidermis. Thus, positional information and cell motility underlie the dispersed patterns of Drosophila Or gene expression.},
	keywords = {Animals, Animals, Genetically Modified, Cell Movement, Drosophila melanogaster, Drosophila Proteins, Epidermis, Gene Expression Regulation, Homeodomain Proteins, Mutation, Nuclear Proteins, Olfactory Receptor Neurons, Receptors, Odorant, Sensilla, Transcription Factors, Transgenes},
	issn = {1878-1551},
	doi = {10.1016/j.devcel.2011.12.015},
	author = {Song, Erin and de Bivort, Benjamin and Dan, Chuntao and Kunes, Sam}
}
@article {662771,
	title = {Reph, a regulator of Eph receptor expression in the Drosophila melanogaster optic lobe.},
	journal = {PLoS One},
	volume = {7},
	number = {5},
	year = {2012},
	month = {2012},
	pages = {e37303},
	abstract = {Receptors of the Eph family of tyrosine kinases and their Ephrin ligands are involved in developmental processes as diverse as angiogenesis, axon guidance and cell migration. However, our understanding of the Eph signaling pathway is incomplete, and could benefit from an analysis by genetic methods. To this end, we performed a genetic modifier screen for mutations that affect Eph signaling in Drosophila melanogaster. Several dozen loci were identified on the basis of their suppression or enhancement of an eye defect induced by the ectopic expression of Ephrin during development; many of these mutant loci were found to disrupt visual system development. One modifier locus, reph (regulator of eph expression), was characterized in molecular detail and found to encode a putative nuclear protein that interacts genetically with Eph signaling pathway mutations. Reph is an autonomous regulator of Eph receptor expression, required for the graded expression of Eph protein and the establishment of an optic lobe axonal topographic map. These results reveal a novel component of the regulatory pathway controlling expression of eph and identify reph as a novel factor in the developing visual system.},
	keywords = {Animals, Drosophila melanogaster, Drosophila Proteins, Female, Gene Expression Regulation, Developmental, Male, Membrane Proteins, Mutation, Nuclear Proteins, Optic Lobe, Nonmammalian, Receptors, Eph Family, Signal Transduction},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0037303},
	author = {Dearborn, Richard E and Dai, Yong and Reed, Brian and Karian, Tamar and Gray, Jessica and Kunes, Sam}
}
@article {8630,
	title = {Determinants of the Drosophila Odorant Receptor Pattern},
	journal = {Developmental Cell},
	volume = {22},
	number = {2},
	year = {2012},
	pages = {363-376},
	author = {Song, E and Kunes, S}
}
@article {8629,
	title = {Reph, a Regulator of Eph Receptor Expression in the Drosophila melanogaster Optic Lobe},
	journal = {PloS },
	volume = {in press},
	year = {2012},
	author = {Dearborn, R.E., Jr. and Y. Dai and Reed, B. and Gray, J. and Kunes, S}
}
@article {662781,
	title = {Endocytic pathway is required for Drosophila Toll innate immune signaling.},
	journal = {Proc Natl Acad Sci U S A},
	volume = {107},
	number = {18},
	year = {2010},
	month = {2010 May 4},
	pages = {8322-7},
	abstract = {The Toll signaling pathway is required for the innate immune response against fungi and Gram-positive bacteria in Drosophila. Here we show that the endosomal proteins Myopic (Mop) and Hepatocyte growth factor-regulated tyrosine kinase substrate (Hrs) are required for the activation of the Toll signaling pathway. This requirement is observed in cultured cells and in flies, and epistasis experiments show that the Mop protein functions upstream of the MyD88 adaptor and the Pelle kinase. Mop and Hrs, which are critical components of the ESCRT-0 endocytosis complex, colocalize with the Toll receptor in endosomes. We conclude that endocytosis is required for the activation of the Toll signaling pathway.},
	keywords = {Animals, Cell Line, Drosophila melanogaster, Drosophila Proteins, Endocytosis, Endosomal Sorting Complexes Required for Transport, Immunity, Innate, Phosphoproteins, Protein Tyrosine Phosphatases, RNA Interference, Signal Transduction, Toll-Like Receptors},
	issn = {1091-6490},
	doi = {10.1073/pnas.1004031107},
	author = {Huang, Hon-Ren and Chen, Zhijian J and Kunes, Sam and Chang, Geen-Dong and Maniatis, Tom}
}
@article {662791,
	title = {The full-length unprocessed hedgehog protein is an active signaling molecule.},
	journal = {J Biol Chem},
	volume = {285},
	number = {4},
	year = {2010},
	month = {2010 Jan 22},
	pages = {2562-8},
	abstract = {The hedgehog (HH) family of ligands plays an important instructional role in metazoan development. HH proteins are initially produced as approximately 45-kDa full-length proteins, which undergo an intramolecular cleavage to generate an amino-terminal product that subsequently becomes cholesterol-modified (HH-Np). It is well accepted that this cholesterol-modified amino-terminal cleavage product is responsible for all HH-dependent signaling events. Contrary to this model we show here that full-length forms of HH proteins are able to traffic to the plasma membrane and participate directly in cell-cell signaling, both in vitro and in vivo. We were also able to rescue a Drosophila eye-specific hh loss of function phenotype by expressing a full-length form of hh that cannot be processed into HH-Np. These results suggest that in some physiological contexts full-length HH proteins may participate directly in HH signaling and that this novel activity of full-length HH may be evolutionarily conserved.},
	keywords = {Animals, Cell Communication, Chick Embryo, Chickens, Drosophila, Drosophila Proteins, Evolution, Molecular, Gene Expression Regulation, Developmental, Hedgehog Proteins, Holoprosencephaly, Humans, Mutagenesis, Site-Directed, Neural Tube, Phenotype, Protein Structure, Tertiary, Protein Transport, Rabbits, Receptors, Cell Surface, Signal Transduction, Structure-Activity Relationship},
	issn = {1083-351X},
	doi = {10.1074/jbc.M109.078626},
	author = {Tokhunts, Robert and Singh, Samer and Chu, Tehyen and D{\textquoteright}Angelo, Gisela and Baubet, Valerie and Goetz, John A and Huang, Zhen and Yuan, Ziqiang and Ascano, Manuel and Zavros, Yana and Th{\'e}rond, Pascal P and Kunes, Sam and Dahmane, Nadia and Robbins, David J}
}
@article {662786,
	title = {Optimizing Drosophila olfactory learning with a semi-automated training device.},
	journal = {J Neurosci Methods},
	volume = {188},
	number = {2},
	year = {2010},
	month = {2010 May 15},
	pages = {195-204},
	abstract = {Drosophila olfactory aversive conditioning has served as a powerful model system with which to elucidate the molecular and neuronal mechanisms underlying memory formation. In the typical protocol, flies are exposed to a constant odor stream while receiving a pulsed electric shock in the conditioning tube of a manual apparatus. We have devised a simple, low-cost semi-automated conditioning apparatus that computationally controls the delivery of odor and shock. A semiconductor-based odor sensor is employed to monitor the change of odor concentration in the training tube. The system thus allows electric shocks to be precisely matched with odor concentration in the training tube. We found that short-term memory performance was improved with a pulsed odor flow protocol, in which odor is presented in short pulses, each paired with electric shock, rather than as a constant flow. The effect of pulsed odor flow might be ascribed to the phenomenon of {\textquoteright}conditioned approach{\textquoteright}, where approach toward an odor is induced when the electric shock is presented before odor pulse ends. Our data shows that the system is applicable to the study of olfactory memory formation and to the examination of conditioning parameters at a level of detail not practical with a manual apparatus.},
	keywords = {Animals, Automation, Avoidance Learning, Brain, Conditioning (Psychology), Drosophila melanogaster, Electric Stimulation, Ethology, Learning, Memory, Neuropsychological Tests, Neuropsychology, Odors, Olfactory Pathways, Smell, Species Specificity, Teaching},
	issn = {1872-678X},
	doi = {10.1016/j.jneumeth.2010.02.007},
	author = {Murakami, Satoshi and Dan, Chuntao and Zagaeski, Brendan and Maeyama, Yuko and Kunes, Sam and Tabata, Tetsuya}
}
@article {5596,
	title = {The full-length unprocessed hedgehog protein is an active signaling molecule.},
	journal = {The Journal of biological chemistry},
	volume = {285},
	number = {4},
	year = {2010},
	note = {n/a
},
	month = {2010 Jan 22},
	pages = {2562-8},
	abstract = {The hedgehog (HH) family of ligands plays an important instructional role in metazoan development. HH proteins are initially produced as approximately 45-kDa full-length proteins, which undergo an intramolecular cleavage to generate an amino-terminal product that subsequently becomes cholesterol-modified (HH-Np). It is well accepted that this cholesterol-modified amino-terminal cleavage product is responsible for all HH-dependent signaling events. Contrary to this model we show here that full-length forms of HH proteins are able to traffic to the plasma membrane and participate directly in cell-cell signaling, both in vitro and in vivo. We were also able to rescue a Drosophila eye-specific hh loss of function phenotype by expressing a full-length form of hh that cannot be processed into HH-Np. These results suggest that in some physiological contexts full-length HH proteins may participate directly in HH signaling and that this novel activity of full-length HH may be evolutionarily conserved.
},
	author = {Tokhunts, Robert and Singh, Samer and Chu, Tehyen and D{\textquoteright}Angelo, Gisela and Baubet, Valerie and Goetz, John A and Huang, Zhen and Yuan, Ziqiang and Ascano, Manuel and Zavros, Yana and Th{\'e}rond, Pascal P and Kunes, Sam and Dahmane, Nadia and Robbins, David J}
}
@article {5595,
	title = {Optimizing Drosophila olfactory learning with a semi-automated training device.},
	journal = {Journal of neuroscience methods},
	volume = {188},
	number = {2},
	year = {2010},
	note = {n/a
},
	month = {2010 May 15},
	pages = {195-204},
	abstract = {Drosophila olfactory aversive conditioning has served as a powerful model system with which to elucidate the molecular and neuronal mechanisms underlying memory formation. In the typical protocol, flies are exposed to a constant odor stream while receiving a pulsed electric shock in the conditioning tube of a manual apparatus. We have devised a simple, low-cost semi-automated conditioning apparatus that computationally controls the delivery of odor and shock. A semiconductor-based odor sensor is employed to monitor the change of odor concentration in the training tube. The system thus allows electric shocks to be precisely matched with odor concentration in the training tube. We found that short-term memory performance was improved with a pulsed odor flow protocol, in which odor is presented in short pulses, each paired with electric shock, rather than as a constant flow. The effect of pulsed odor flow might be ascribed to the phenomenon of {\textquoteright}conditioned approach{\textquoteright}, where approach toward an odor is induced when the electric shock is presented before odor pulse ends. Our data shows that the system is applicable to the study of olfactory memory formation and to the examination of conditioning parameters at a level of detail not practical with a manual apparatus.
},
	author = {Murakami, Satoshi and Dan, Chuntao and Zagaeski, Brendan and Maeyama, Yuko and Kunes, Sam and Tabata, Tetsuya}
}
@article {5594,
	title = {Endocytic pathway is required for Drosophila Toll innate immune signaling.},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {107},
	number = {18},
	year = {2010},
	note = {n/a
},
	month = {2010 May 4},
	pages = {8322-7},
	abstract = {The Toll signaling pathway is required for the innate immune response against fungi and Gram-positive bacteria in Drosophila. Here we show that the endosomal proteins Myopic (Mop) and Hepatocyte growth factor-regulated tyrosine kinase substrate (Hrs) are required for the activation of the Toll signaling pathway. This requirement is observed in cultured cells and in flies, and epistasis experiments show that the Mop protein functions upstream of the MyD88 adaptor and the Pelle kinase. Mop and Hrs, which are critical components of the ESCRT-0 endocytosis complex, colocalize with the Toll receptor in endosomes. We conclude that endocytosis is required for the activation of the Toll signaling pathway.
},
	author = {Huang, Hon-Ren and Chen, Zhijian J and Kunes, Sam and Chang, Geen-Dong and Maniatis, Tom}
}
@article {662796,
	title = {Amino acid metabolic origin as an evolutionary influence on protein sequence in yeast.},
	journal = {J Mol Evol},
	volume = {68},
	number = {5},
	year = {2009},
	month = {2009 May},
	pages = {490-7},
	abstract = {The metabolic cycle of Saccharomyces cerevisiae consists of alternating oxidative (respiration) and reductive (glycolysis) energy-yielding reactions. The intracellular concentrations of amino acid precursors generated by these reactions oscillate accordingly, attaining maximal concentration during the middle of their respective yeast metabolic cycle phases. Typically, the amino acids themselves are most abundant at the end of their precursor{\textquoteright}s phase. We show that this metabolic cycling has likely biased the amino acid composition of proteins across the S. cerevisiae genome. In particular, we observed that the metabolic source of amino acids is the single most important source of variation in the amino acid compositions of functionally related proteins and that this signal appears only in (facultative) organisms using both oxidative and reductive metabolism. Periodically expressed proteins are enriched for amino acids generated in the preceding phase of the metabolic cycle. Proteins expressed during the oxidative phase contain more glycolysis-derived amino acids, whereas proteins expressed during the reductive phase contain more respiration-derived amino acids. Rare amino acids (e.g., tryptophan) are greatly overrepresented or underrepresented, relative to the proteomic average, in periodically expressed proteins, whereas common amino acids vary by a few percent. Genome-wide, we infer that 20,000 to 60,000 residues have been modified by this previously unappreciated pressure. This trend is strongest in ancient proteins, suggesting that oscillating endogenous amino acid availability exerted genome-wide selective pressure on protein sequences across evolutionary time.},
	keywords = {Amino Acid Sequence, Amino Acids, Bias (Epidemiology), Evolution, Molecular, Genetic Variation, Molecular Sequence Data, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Sequence Analysis, Protein},
	issn = {1432-1432},
	doi = {10.1007/s00239-009-9218-5},
	author = {de Bivort, Benjamin L and Perlstein, Ethan O and Kunes, Sam and Schreiber, Stuart L}
}
@article {5597,
	title = {Amino acid metabolic origin as an evolutionary influence on protein sequence in yeast.},
	journal = {Journal of molecular evolution},
	volume = {68},
	number = {5},
	year = {2009},
	note = {n/a
},
	month = {2009 May},
	pages = {490-7},
	abstract = {The metabolic cycle of Saccharomyces cerevisiae consists of alternating oxidative (respiration) and reductive (glycolysis) energy-yielding reactions. The intracellular concentrations of amino acid precursors generated by these reactions oscillate accordingly, attaining maximal concentration during the middle of their respective yeast metabolic cycle phases. Typically, the amino acids themselves are most abundant at the end of their precursor{\textquoteright}s phase. We show that this metabolic cycling has likely biased the amino acid composition of proteins across the S. cerevisiae genome. In particular, we observed that the metabolic source of amino acids is the single most important source of variation in the amino acid compositions of functionally related proteins and that this signal appears only in (facultative) organisms using both oxidative and reductive metabolism. Periodically expressed proteins are enriched for amino acids generated in the preceding phase of the metabolic cycle. Proteins expressed during the oxidative phase contain more glycolysis-derived amino acids, whereas proteins expressed during the reductive phase contain more respiration-derived amino acids. Rare amino acids (e.g., tryptophan) are greatly overrepresented or underrepresented, relative to the proteomic average, in periodically expressed proteins, whereas common amino acids vary by a few percent. Genome-wide, we infer that 20,000 to 60,000 residues have been modified by this previously unappreciated pressure. This trend is strongest in ancient proteins, suggesting that oscillating endogenous amino acid availability exerted genome-wide selective pressure on protein sequences across evolutionary time.
},
	author = {de Bivort, Benjamin L and Perlstein, Ethan O and Kunes, Sam and Schreiber, Stuart L}
}
@article {5598,
	title = {Evolutionarily conserved optimization of amino acid biosynthesis.},
	journal = {Journal of molecular evolution},
	volume = {65},
	number = {2},
	year = {2007},
	note = {n/a
},
	month = {2007 Aug},
	pages = {186-96},
	abstract = {The "cognate bias hypothesis" states that early in evolutionary history the biosynthetic enzymes for amino acid x gradually lost residues of x, thereby reducing the threshold for deleterious effects of x scarcity. The resulting reduction in cognate amino acid composition of the enzymes comprising a particular amino acid biosynthetic pathway is predicted to confer a selective growth advantage on cells. Bioinformatic evidence from protein-sequence data of two bacterial species previously demonstrated reduced cognate bias in amino acid biosynthetic pathways. Here we show that cognate bias in amino acid biosynthesis is present in the other domains of life-Archaebacteria and Eukaryota. We also observe evolutionarily conserved underrepresentations (e.g., glycine in methionine biosynthesis) and overrepresentations (e.g., tryptophan in asparagine biosynthesis) of amino acids in noncognate biosynthetic pathways, which can be explained by secondary amino acid metabolism. Additionally, we experimentally validate the cognate bias hypothesis using the yeast Saccharomyces cerevisiae. Specifically, we show that the degree to which growth declines following amino acid deprivation is negatively correlated with the degree to which an amino acid is underrepresented in the enzymes that comprise its cognate biosynthetic pathway. Moreover, we demonstrate that cognate fold representation is more predictive of growth advantage than a host of other potential growth-limiting factors, including an amino acid{\textquoteright}s metabolic cost or its intracellular concentration and compartmental distribution.
},
	author = {Perlstein, Ethan O and de Bivort, Benjamin L and Kunes, Samuel and Schreiber, Stuart L}
}
@article {662806,
	title = {A C-terminal motif targets Hedgehog to axons, coordinating assembly of the Drosophila eye and brain.},
	journal = {Dev Cell},
	volume = {10},
	number = {5},
	year = {2006},
	month = {2006 May},
	pages = {635-46},
	abstract = {The developmental signal Hedgehog is distributed to two receptive fields by the photoreceptor neurons of the developing Drosophila retina. Delivery to the retina propagates ommatidial development across a precursor field. Transport along photoreceptor axons induces the development of postsynaptic neurons in the brain. Hedgehog is composed of N-terminal and C-terminal domains that dissociate in an autoproteolytic reaction that attaches cholesterol to the N-terminal cleavage product. Here, we show that the N-terminal domain is targeted to the retina when synthesized in the absence of the C-terminal domain. In contrast to studies that have focused on cholesterol as a determinant of subcellular localization, we find that the C-terminal domain harbors a conserved motif that overrides retinal localization, sending most of the autocleavage products into vesicles bound for growth cones or synapses. Competition between targeting signals at the opposite ends of Hedgehog apparently controls the match between eye and brain development.},
	keywords = {Amino Acid Motifs, Amino Acid Sequence, Animals, Axons, Brain, Drosophila melanogaster, Drosophila Proteins, Gene Expression Regulation, Developmental, Growth Cones, Hedgehog Proteins, Molecular Sequence Data, Photoreceptor Cells, Invertebrate, Protein Processing, Post-Translational, Protein Transport, Retina, Signal Transduction, Synaptotagmins, Transport Vesicles},
	issn = {1534-5807},
	doi = {10.1016/j.devcel.2006.03.003},
	author = {Chu, Tehyen and Chiu, Michael and Zhang, Elisa and Kunes, Sam}
}
@article {662811,
	title = {Synaptic protein synthesis associated with memory is regulated by the RISC pathway in Drosophila.},
	journal = {Cell},
	volume = {124},
	number = {1},
	year = {2006},
	month = {2006 Jan 13},
	pages = {191-205},
	abstract = {Long-lasting forms of memory require protein synthesis, but how the pattern of synthesis is related to the storage of a memory has not been determined. Here we show that neural activity directs the mRNA of the Drosophila Ca(2+), Calcium/Calmodulin-dependent Kinase II (CaMKII), to postsynaptic sites, where it is rapidly translated. These features of CaMKII synthesis are recapitulated during the induction of a long-term memory and produce patterns of local protein synthesis specific to the memory. We show that mRNA transport and synaptic protein synthesis are regulated by components of the RISC pathway, including the SDE3 helicase Armitage, which is specifically required for long-lasting memory. Armitage is localized to synapses and lost in a memory-specific pattern that is inversely related to the pattern of synaptic protein synthesis. Therefore, we propose that degradative control of the RISC pathway underlies the pattern of synaptic protein synthesis associated with a stable memory.},
	keywords = {Amino Acid Sequence, Animals, Calcium, Calcium-Calmodulin-Dependent Protein Kinase Type 2, Calcium-Calmodulin-Dependent Protein Kinases, Drosophila, Gene Expression Regulation, Memory, Models, Neurological, Molecular Sequence Data, Neurons, Protein Biosynthesis, RNA, Messenger, RNA-Induced Silencing Complex, Synapses, Synaptic Transmission},
	issn = {0092-8674},
	doi = {10.1016/j.cell.2005.12.017},
	author = {Ashraf, Shovon I and McLoon, Anna L and Sclarsic, Sarah M and Kunes, Sam}
}
@article {662801,
	title = {A trace of silence: memory and microRNA at the synapse.},
	journal = {Curr Opin Neurobiol},
	volume = {16},
	number = {5},
	year = {2006},
	month = {2006 Oct},
	pages = {535-9},
	abstract = {Identifying the neural circuits that mediate particular behaviors and uncovering their plasticity is an endeavor at the heart of neuroscience. This effort is allied with the elucidation of plasticity mechanisms, because the molecular determinants of plasticity can be markers for the neurons and synapses that are modified by experience. Of particular interest is protein synthesis localized to the synapse, which might establish and maintain the stable modification of neuronal properties, including the pattern and strength of synaptic connections. Recent studies reveal that microRNAs and the RISC pathway regulate synaptic protein synthesis. Is synaptic activity of the RISC pathway a molecular signature of memory?},
	keywords = {Animals, Brain, Gene Expression, Gene Expression Regulation, Humans, Memory, MicroRNAs, Neuronal Plasticity, Protein Biosynthesis, RNA-Induced Silencing Complex, Synapses},
	issn = {0959-4388},
	doi = {10.1016/j.conb.2006.08.007},
	author = {Ashraf, Shovon I and Kunes, Sam}
}
@article {5601,
	title = {Synaptic protein synthesis associated with memory is regulated by the RISC pathway in Drosophila.},
	journal = {Cell},
	volume = {124},
	number = {1},
	year = {2006},
	note = {n/a
},
	month = {2006 Jan 13},
	pages = {191-205},
	abstract = {Long-lasting forms of memory require protein synthesis, but how the pattern of synthesis is related to the storage of a memory has not been determined. Here we show that neural activity directs the mRNA of the Drosophila Ca(2+), Calcium/Calmodulin-dependent Kinase II (CaMKII), to postsynaptic sites, where it is rapidly translated. These features of CaMKII synthesis are recapitulated during the induction of a long-term memory and produce patterns of local protein synthesis specific to the memory. We show that mRNA transport and synaptic protein synthesis are regulated by components of the RISC pathway, including the SDE3 helicase Armitage, which is specifically required for long-lasting memory. Armitage is localized to synapses and lost in a memory-specific pattern that is inversely related to the pattern of synaptic protein synthesis. Therefore, we propose that degradative control of the RISC pathway underlies the pattern of synaptic protein synthesis associated with a stable memory.
},
	author = {Ashraf, Shovon I and McLoon, Anna L and Sclarsic, Sarah M and Kunes, Sam}
}
@article {5600,
	title = {A C-terminal motif targets Hedgehog to axons, coordinating assembly of the Drosophila eye and brain.},
	journal = {Developmental cell},
	volume = {10},
	number = {5},
	year = {2006},
	note = {n/a
},
	month = {2006 May},
	pages = {635-46},
	abstract = {The developmental signal Hedgehog is distributed to two receptive fields by the photoreceptor neurons of the developing Drosophila retina. Delivery to the retina propagates ommatidial development across a precursor field. Transport along photoreceptor axons induces the development of postsynaptic neurons in the brain. Hedgehog is composed of N-terminal and C-terminal domains that dissociate in an autoproteolytic reaction that attaches cholesterol to the N-terminal cleavage product. Here, we show that the N-terminal domain is targeted to the retina when synthesized in the absence of the C-terminal domain. In contrast to studies that have focused on cholesterol as a determinant of subcellular localization, we find that the C-terminal domain harbors a conserved motif that overrides retinal localization, sending most of the autocleavage products into vesicles bound for growth cones or synapses. Competition between targeting signals at the opposite ends of Hedgehog apparently controls the match between eye and brain development.
},
	author = {Chu, Tehyen and Chiu, Michael and Zhang, Elisa and Kunes, Sam}
}
@article {5599,
	title = {A trace of silence: memory and microRNA at the synapse.},
	journal = {Current opinion in neurobiology},
	volume = {16},
	number = {5},
	year = {2006},
	note = {n/a
},
	month = {2006 Oct},
	pages = {535-9},
	abstract = {Identifying the neural circuits that mediate particular behaviors and uncovering their plasticity is an endeavor at the heart of neuroscience. This effort is allied with the elucidation of plasticity mechanisms, because the molecular determinants of plasticity can be markers for the neurons and synapses that are modified by experience. Of particular interest is protein synthesis localized to the synapse, which might establish and maintain the stable modification of neuronal properties, including the pattern and strength of synaptic connections. Recent studies reveal that microRNAs and the RISC pathway regulate synaptic protein synthesis. Is synaptic activity of the RISC pathway a molecular signature of memory?
},
	author = {Ashraf, Shovon I and Kunes, Sam}
}
@article {3076,
	title = {A C-terminal motif targets hedgehog to axons, coordinating assembly of the Drosophila eye and brain},
	journal = {Developmental Cell},
	volume = {10},
	number = {5},
	year = {2006},
	month = {05/2006},
	pages = {635-46},
	abstract = {The developmental signal Hedgehog is distributed to two receptive fields by the photoreceptor neurons of the developing Drosophila retina. Delivery to the retina propagates ommatidial development across a precursor field. Transport along photoreceptor axons induces the development of postsynaptic neurons in the brain. Hedgehog is composed of N-terminal and C-terminal domains that dissociate in an autoproteolytic reaction that attaches cholesterol to the N-terminal cleavage product. Here, we show that the N-terminal domain is targeted to the retina when synthesized in the absence of the C-terminal domain. In contrast to studies that have focused on cholesterol as a determinant of subcellular localization, we find that the C-terminal domain harbors a conserved motif that overrides retinal localization, sending most of the autocleavage products into vesicles bound for growth cones or synapses. Competition between targeting signals at the opposite ends of Hedgehog apparently controls the match between eye and brain development.
},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16678778},
	author = {Kunes, S and T. Chu and M. Chiu and E. Zhang}
}
@article {662821,
	title = {An axon scaffold induced by retinal axons directs glia to destinations in the Drosophila optic lobe.},
	journal = {Development},
	volume = {131},
	number = {10},
	year = {2004},
	month = {2004 May},
	pages = {2291-303},
	abstract = {In the developing Drosophila visual system, glia migrate into stereotyped positions within the photoreceptor axon target fields and provide positional information for photoreceptor axon guidance. Glial migration conversely depends on photoreceptor axons, as glia precursors stall in their progenitor zones when retinal innervation is eliminated. Our results support the view that this requirement for retinal innervation reflects a role of photoreceptor axons in the establishment of an axonal scaffold that guides glial cell migration. Optic lobe cortical axons extend from dorsal and ventral positions towards incoming photoreceptor axons and establish at least four separate pathways that direct glia to proper destinations in the optic lobe neuropiles. Photoreceptor axons induce the outgrowth of these scaffold axons. Most glia do not migrate when the scaffold axons are missing. Moreover, glia follow the aberrant pathways of scaffold axons that project aberrantly, as occurs in the mutant dachsous. The local absence of glia is accompanied by extensive apoptosis of optic lobe cortical neurons. These observations reveal a mechanism for coordinating photoreceptor axon arrival in the brain with the distribution of glia to multiple target destinations, where they are required for axon guidance and neuronal survival.},
	keywords = {Animals, Axons, Body Patterning, Cell Movement, Cell Survival, Drosophila melanogaster, Morphogenesis, Neuroglia, Optic Lobe, Nonmammalian},
	issn = {0950-1991},
	doi = {10.1242/dev.01111},
	author = {Dearborn, Richard and Kunes, Sam}
}
@article {662816,
	title = {Nonvesicular release of acetylcholine is required for axon targeting in the Drosophila visual system.},
	journal = {Proc Natl Acad Sci U S A},
	volume = {101},
	number = {42},
	year = {2004},
	month = {2004 Oct 19},
	pages = {15213-8},
	abstract = {We report evidence for a developmental role of acetylcholine in axon pathfinding in the Drosophila visual system. Acetylcholine was detected on photoreceptor axons during their navigation to target sites in the brain, a time well before the formation of functional synapses. The pattern of photoreceptor axon projections was severely disrupted when acetylcholine synthesis or metabolism was altered or eliminated, or when transgenic alpha-bungarotoxin, a nicotinic acetylcholine receptor antagonist, was expressed in the developing eye or brain. The requirement for acetylcholine signaling exists before photoreceptor neurons form synaptic connections and does not require the function of vesicular acetylcholine transporter protein. That this early effect of acetylcholine is mediated through nonvesicular release is further supported by the observation that transgenic expression of tetanus toxin, a blocker of neurotransmitter release via synaptic vesicles, did not cause similar photoreceptor axon projection defects. These observations support the notion that a form of acetylcholine secretion mediates the behavior of growth cones during axon pathfinding.},
	keywords = {Acetylcholine, Acetylcholinesterase, Animals, Animals, Genetically Modified, Axons, Brain, Bungarotoxins, Choline O-Acetyltransferase, Drosophila, Eye, Gene Expression Regulation, Developmental, Mosaicism, Ocular Physiological Phenomena, Phenotype, Photoreceptor Cells, Invertebrate, Recombinant Proteins},
	issn = {0027-8424},
	doi = {10.1073/pnas.0308141101},
	author = {Yang, Hong and Kunes, Sam}
}
@article {5603,
	title = {An axon scaffold induced by retinal axons directs glia to destinations in the Drosophila optic lobe.},
	journal = {Development (Cambridge, England)},
	volume = {131},
	number = {10},
	year = {2004},
	note = {n/a
},
	month = {2004 May},
	pages = {2291-303},
	abstract = {In the developing Drosophila visual system, glia migrate into stereotyped positions within the photoreceptor axon target fields and provide positional information for photoreceptor axon guidance. Glial migration conversely depends on photoreceptor axons, as glia precursors stall in their progenitor zones when retinal innervation is eliminated. Our results support the view that this requirement for retinal innervation reflects a role of photoreceptor axons in the establishment of an axonal scaffold that guides glial cell migration. Optic lobe cortical axons extend from dorsal and ventral positions towards incoming photoreceptor axons and establish at least four separate pathways that direct glia to proper destinations in the optic lobe neuropiles. Photoreceptor axons induce the outgrowth of these scaffold axons. Most glia do not migrate when the scaffold axons are missing. Moreover, glia follow the aberrant pathways of scaffold axons that project aberrantly, as occurs in the mutant dachsous. The local absence of glia is accompanied by extensive apoptosis of optic lobe cortical neurons. These observations reveal a mechanism for coordinating photoreceptor axon arrival in the brain with the distribution of glia to multiple target destinations, where they are required for axon guidance and neuronal survival.
},
	author = {Dearborn, Richard and Kunes, Sam}
}
@article {5602,
	title = {Nonvesicular release of acetylcholine is required for axon targeting in the Drosophila visual system.},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {101},
	number = {42},
	year = {2004},
	note = {n/a
},
	month = {2004 Oct 19},
	pages = {15213-8},
	abstract = {We report evidence for a developmental role of acetylcholine in axon pathfinding in the Drosophila visual system. Acetylcholine was detected on photoreceptor axons during their navigation to target sites in the brain, a time well before the formation of functional synapses. The pattern of photoreceptor axon projections was severely disrupted when acetylcholine synthesis or metabolism was altered or eliminated, or when transgenic alpha-bungarotoxin, a nicotinic acetylcholine receptor antagonist, was expressed in the developing eye or brain. The requirement for acetylcholine signaling exists before photoreceptor neurons form synaptic connections and does not require the function of vesicular acetylcholine transporter protein. That this early effect of acetylcholine is mediated through nonvesicular release is further supported by the observation that transgenic expression of tetanus toxin, a blocker of neurotransmitter release via synaptic vesicles, did not cause similar photoreceptor axon projection defects. These observations support the notion that a form of acetylcholine secretion mediates the behavior of growth cones during axon pathfinding.
},
	author = {Yang, Hong and Kunes, Sam}
}
@article {662826,
	title = {Eph receptor tyrosine kinase-mediated formation of a topographic map in the Drosophila visual system.},
	journal = {J Neurosci},
	volume = {22},
	number = {4},
	year = {2002},
	month = {2002 Feb 15},
	pages = {1338-49},
	abstract = {Roles for Eph receptor tyrosine kinase signaling in the formation of topographic patterns of axonal connectivity have been well established in vertebrate visual systems. Here we describe a role for a Drosophila Eph receptor tyrosine kinase (EPH) in the control of photoreceptor axon and cortical axon topography in the developing visual system. Although uniform across the developing eye, EPH is expressed in a concentration gradient appropriate for conveying positional information during cortical axon guidance in the second-order optic ganglion, the medulla. Disruption of this graded pattern of EPH activity by double-stranded RNA interference or by ectopic expression of wild-type or dominant-negative transgenes perturbed the establishment of medulla cortical axon topography. In addition, abnormal midline fasciculation of photoreceptor axons resulted from the eye-specific expression of the dominant-negative EPH transgene. These observations reveal a conserved role for Eph kinases as determinants of topographic map formation in vertebrates and invertebrates.},
	keywords = {Animals, Animals, Genetically Modified, Axons, Brain Mapping, Cell Differentiation, Cloning, Molecular, Crosses, Genetic, Drosophila, Ganglia, Invertebrate, Gene Expression Regulation, Developmental, Genes, Dominant, Growth Cones, Immunohistochemistry, In Situ Hybridization, Molecular Sequence Data, Morphogenesis, Neurons, Phenotype, Photoreceptor Cells, Invertebrate, Receptor Protein-Tyrosine Kinases, Receptor, EphA1, RNA, Double-Stranded, RNA, Messenger, Synapses, Transgenes, Visual Pathways},
	issn = {1529-2401},
	author = {Dearborn, Richard and He, Qi and Kunes, Sam and Dai, Yong}
}
@article {5604,
	title = {Eph receptor tyrosine kinase-mediated formation of a topographic map in the Drosophila visual system.},
	journal = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	volume = {22},
	number = {4},
	year = {2002},
	note = {n/a
},
	month = {2002 Feb 15},
	pages = {1338-49},
	abstract = {Roles for Eph receptor tyrosine kinase signaling in the formation of topographic patterns of axonal connectivity have been well established in vertebrate visual systems. Here we describe a role for a Drosophila Eph receptor tyrosine kinase (EPH) in the control of photoreceptor axon and cortical axon topography in the developing visual system. Although uniform across the developing eye, EPH is expressed in a concentration gradient appropriate for conveying positional information during cortical axon guidance in the second-order optic ganglion, the medulla. Disruption of this graded pattern of EPH activity by double-stranded RNA interference or by ectopic expression of wild-type or dominant-negative transgenes perturbed the establishment of medulla cortical axon topography. In addition, abnormal midline fasciculation of photoreceptor axons resulted from the eye-specific expression of the dominant-negative EPH transgene. These observations reveal a conserved role for Eph kinases as determinants of topographic map formation in vertebrates and invertebrates.
},
	author = {Dearborn, Richard and He, Qi and Kunes, Sam and Dai, Yong}
}
@article {5606,
	title = {Axonal signals in the assembly of neural circuitry.},
	journal = {Current opinion in neurobiology},
	volume = {10},
	number = {1},
	year = {2000},
	note = {n/a
},
	month = {2000 Feb},
	pages = {58-62},
	abstract = {Recent work in Drosophila and rodents has revealed that proteins transported along axons and delivered to pathway and target cell populations play important roles in the construction of neural circuitry. Interestingly, the parallels between these systems may extend to the identities of some of the molecules involved.
},
	author = {Kunes, S}
}
@article {5605,
	title = {Combgap relays wingless signal reception to the determination of cortical cell fate in the Drosophila visual system.},
	journal = {Molecular cell},
	volume = {6},
	number = {5},
	year = {2000},
	note = {n/a
},
	month = {2000 Nov},
	pages = {1143-54},
	abstract = {The dorsoventral axis of the Drosophila visual cortex is patterned by nonautonomous signals expressed at its dorsal and ventral margins. wingless (wg) expression at the margins induces decapentaplegic (dpp), optomotor blind (omb), and aristaless in adjacent domains. We show that Combgap, a zinc finger protein, represses Wg target gene expression in the visual cortex. Wg signal reception downregulates combgap expression and derepresses target gene transcription. Combgap participates in a Hedgehog-controlled circuit in the developing wing and leg by regulating the expression of Cubitus interruptus. Combgap is thus a tissue-specific relay between Wingless and its target genes for the determination of cell fate in the visual cortex.
},
	author = {Song, Y and S. Chung and Kunes, S}
}
@article {5607,
	title = {Stop or go in the target zone.},
	journal = {Neuron},
	volume = {22},
	number = {4},
	year = {1999},
	note = {n/a
},
	month = {1999 Apr},
	pages = {639-40},
	abstract = {n/a},
	author = {Kunes, S}
}
@article {5609,
	title = {A retinal axon fascicle uses spitz, an EGF receptor ligand, to construct a synaptic cartridge in the brain of Drosophila.},
	journal = {Cell},
	volume = {95},
	number = {5},
	year = {1998},
	note = {n/a
},
	month = {1998 Nov 25},
	pages = {693-703},
	abstract = {Photoreceptor axons arriving in the Drosophila brain organize their postsynaptic target field into a precise array of five neuron "cartridge" ensembles. Here we show that Hedgehog, an initial inductive signal transported along retinal axons from the developing eye, induces postsynaptic precursor cells to express the Drosophila homolog of the epidermal growth factor receptor (EGFR). The EGFR ligand Spitz, a signal for ommatidial assembly in the compound eye, is transported to retinal axon termini in the brain where it acts as a local cue for the recruitment of five cells into a cartridge ensemble. Hedgehog and Spitz thus bring about the concerted assembly of ommatidial and synaptic cartridge units, imposing the "neurocrystalline" order of the compound eye on the postsynaptic target field.
},
	author = {Huang, Z and Shilo, B Z and Kunes, S}
}
@article {5608,
	title = {Signals transmitted along retinal axons in Drosophila: Hedgehog signal reception and the cell circuitry of lamina cartridge assembly.},
	journal = {Development (Cambridge, England)},
	volume = {125},
	number = {19},
	year = {1998},
	note = {n/a
},
	month = {1998 Oct},
	pages = {3753-64},
	abstract = {The arrival of retinal axons in the brain of Drosophila triggers the assembly of glial and neuronal precursors into a {\textquoteright}neurocrystalline{\textquoteright} array of lamina synaptic {\textquoteright}cartridges{\textquoteright}. Hedgehog, a secreted protein, is an inductive signal delivered by retinal axons for the initial steps of lamina differentiation. In the development of many tissues, Hedgehog acts in a signal relay cascade via the induction of secondary secreted factors. Here we show that lamina neuronal precursors respond directly to Hedgehog signal reception by entering S-phase, a step that is controlled by the Hedgehog-dependent transcriptional regulator Cubitus interruptus. The terminal differentiation of neuronal precursors and the migration and differentiation of glia appear to be controlled by other retinal axon-mediated signals. Thus retinal axons impose a program of developmental events on their postsynaptic field utilizing distinct signals for different precursor populations.
},
	author = {Huang, Z and Kunes, S}
}
@article {5610,
	title = {Hedgehog, transmitted along retinal axons, triggers neurogenesis in the developing visual centers of the Drosophila brain.},
	journal = {Cell},
	volume = {86},
	number = {3},
	year = {1996},
	note = {n/a
},
	month = {1996 Aug 9},
	pages = {411-22},
	abstract = {The development of the visual centers of the Drosophila brain is tightly regulated by the ingrowth of retinal axons from the developing eye. In the first optic ganglion, the lamina, arriving retinal axons trigger the precursors of their synaptic partners to complete a final cell division and commence neural differentiation. The secreted product of the hedgehog gene regulates the temporal assembly of photoreceptor precursor cells into ommatidial clusters in the compound eye. Here, we show that Hedgehog is transmitted along the retinal axons to serve as the inductive signal in the brain. Hedgehog acts in the first of two retinal axon-mediated steps in the assembly of lamina synaptic cartridges. These observations provide a novel insight into the molecular interactions that orchestrate the assembly of neural precursor cells into precise synaptic circuits.
},
	author = {Huang, Z and Kunes, S}
}
@article {5611,
	title = {Pattern formation in the visual centers of the Drosophila brain: wingless acts via decapentaplegic to specify the dorsoventral axis.},
	journal = {Cell},
	volume = {78},
	number = {3},
	year = {1994},
	note = {n/a
},
	month = {1994 Aug 12},
	pages = {437-48},
	abstract = {A stepwise morphogenetic program of cell division and cell fate determination generates the precise neuronal architecture of the visual centers of the Drosophila brain. Here, we show that the assembly of the target structure for ingrowing retinal axons involves cell-cell interactions mediated by the secreted product of the wingless (wg) gene. wg, expressed in two symmetrical domains of the developing brain, is required to induce and maintain the expression of the secreted decapentaplegic (dpp) gene product in adjacent domains. wg and dpp function are required for target field neurons to adopt their proper fates and to send axons into the developing target structure. These observations implicate a cascade of diffusible signaling molecules in patterning the visual centers of the Drosophila brain.
},
	author = {Kaphingst, K and Kunes, S}
}
@article {5613,
	title = {Topography in the Drosophila visual system.},
	journal = {Current opinion in neurobiology},
	volume = {3},
	number = {1},
	year = {1993},
	note = {n/a
},
	month = {1993 Feb},
	pages = {53-9},
	abstract = {The Drosophila visual system offers an excellent opportunity for studying the development of proper retinotopic connections at the level of individual identifiable cell types. Recent work suggests that, despite obvious anatomical and developmental differences, at least some of the general developmental strategies operating in the Drosophila visual system parallel observations made previously for vertebrates. The extensive repertoire of powerful genetic and molecular techniques available in Drosophila can now be directed towards determining whether these parallels also reflect similarities in the underlying molecular mechanisms.
},
	author = {Kunes, S and Steller, H}
}
@article {5612,
	title = {Independent guidance of retinal axons in the developing visual system of Drosophila.},
	journal = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	volume = {13},
	number = {2},
	year = {1993},
	note = {n/a
},
	month = {1993 Feb},
	pages = {752-67},
	abstract = {The development of the adult visual system of Drosophila requires the establishment of precise retinotopic connections between retinal photoreceptor cell axons and their synaptic partners in the optic lobe of the brain. To assess the role of axon-axon interactions in retinal axon guidance, we used genetic methods to disrupt the normal spatiotemporal order of retinal axon ingrowth. We examined retinal axon projections to the developing first optic ganglion, the lamina, in two mutants in which reduced numbers of ommatidia develop in the eye imaginal disk. We find that in the developing lamina of these mutants, sine oculis and Ellipse, retinal axons project to proper dorsoventral positions despite the absence of the usual array of neighboring retinal axons. In a second approach, we examined animals that were somatic mosaics for the mutation, glass. In glass- animals, retinal axons project aberrantly and the larval optic nerve is absent. We find that in the developing lamina of glass mosaic animals, wild-type retinal axons project to proper dorsoventral positions despite the misrouted projections of neighboring glass- retinal axons. In addition, wild-type retinal axons project normally in the absence of the larval optic nerve, indicating that the latter is not an essential pioneer for retinal axon navigation. Our observations support the proposal that axon fascicles can make at least some pathfinding decisions independently of other retinal axon fascicles. We suggest that positional guidance cues that might label axon pathways and target destinations contribute to retinotopic pattern formation in the Drosophila visual system.
},
	author = {Kunes, S and Wilson, C. and Steller, H}
}
@article {5614,
	title = {Ablation of Drosophila photoreceptor cells by conditional expression of a toxin gene.},
	journal = {Genes \& development},
	volume = {5},
	number = {6},
	year = {1991},
	note = {n/a
},
	month = {1991 Jun},
	pages = {970-83},
	abstract = {We have used toxin-mediated ablation to study some aspects of visual system development in Drosophila melanogaster. To devise a method that permits the conditional expression of a cellular toxin, we introduced an amber mutation into the diphtheria toxin-A-chain gene. In transgenic animals, this toxin gene can be activated by providing the gene for an amber suppressor tRNA. By coupling this toxin gene to the photoreceptor cell-specific promoter of the chaoptic gene, photoreceptor cells could be specifically ablated during development. Photoreceptor cell-specific markers normally activated during pupal development failed to appear after midpupation. Photoreceptor cells were absent from the retinas of adult flies at eclosion. We have assessed the consequences of photoreceptor cell ablation for eye and optic lobe development. We suggest that the larval photoreceptor nerve is not essential, in the late larval stages, for retinula photoreceptor cell axons to achieve their proper projection pattern in the brain. Moreover, while retinula photoreceptor innervation is initially required for the development of normal optic ganglia, the ablation of these cells in midpupation has no discernible effect. This approach to cell-specific ablation should be generally applicable to the study of cellular functions in development and behavior.
},
	author = {Kunes, S and Steller, H}
}
@article {5615,
	title = {Synapsis-mediated fusion of free DNA ends forms inverted dimer plasmids in yeast.},
	journal = {Genetics},
	volume = {124},
	number = {1},
	year = {1990},
	note = {n/a
},
	month = {1990 Jan},
	pages = {67-80},
	abstract = {When yeast (Saccharomyces cerevisiae) is transformed with linearized plasmid DNA and the ends of the plasmid do not share homology with the yeast genome, circular inverted (head-to-head) dimer plasmids are the principal product of repair. By measurements of the DNA concentration dependence of transformation with a linearized plasmid, and by transformation with mixtures of genetically marked plasmids, we show that two plasmid molecules are required to form an inverted dimer plasmid. Several observations suggest that homologous pairing accounts for the head-to-head joining of the two plasmid molecules. First, an enhanced frequency of homologous recombination is detected when genetically marked plasmids undergo end-to-end fusion. Second, when a plasmid is linearized within an inverted repeat, such that its ends could undergo head-to-tail homologous pairing, it is repaired by intramolecular head-to-tail joining. Last, in the joining of homologous linearized plasmids of different length, a shorter molecule can acquire a longer plasmid end by homologous recombination. The formation of inverted dimer plasmids may be related to some forms of chromosomal rearrangement. These might include the fusion of broken sister chromatids in the bridge-breakage-fusion cycle and the head-to-head duplication of genomic DNA at the sites of gene amplifications.
},
	author = {Kunes, S and Botstein, D and Fox, M S}
}
@article {5616,
	title = {Fine structure recombinational analysis of cloned genes using yeast transformation.},
	journal = {Genetics},
	volume = {115},
	number = {1},
	year = {1987},
	note = {n/a
},
	month = {1987 Jan},
	pages = {73-81},
	abstract = {We describe a general method for analyzing the genetic fine structure of plasmid-borne genes in yeast. Previously we had reported that a linearized plasmid is efficiently rescued by recombination with a homologous restriction fragment when these are co-introduced by DNA-mediated transformation of yeast. Here, we show that a mutation can be localized to a small DNA interval when members of a deletion series of wild-type restriction fragments are used in the rescue of a linearized mutant plasmid. The resolution of this method is to at least 30 base pairs and is limited by the loss of a wild-type marker with proximity to a free DNA end. As a means for establishing the nonidentity of two mutations, we determined the resolution of two-point crosses with a mutant linearized plasmid and a mutant homologous restriction fragment. Recombination between mutations separated by as little as 100 base pairs was detected. Moreover, the results indicate that exchange within a marked interval results primarily from one of two single crossovers that repair the linearized plasmid. These approaches to mapping the genetic fine structure of plasmids should join existing methods in a robust approach to the mutational analysis of gene structure in yeast.
},
	author = {Kunes, S and Ma, H and Overbye, K and Fox, M S and Botstein, D}
}
@article {5617,
	title = {Plasmid construction by homologous recombination in yeast.},
	journal = {Gene},
	volume = {58},
	number = {2-3},
	year = {1987},
	note = {n/a
},
	month = {1987},
	pages = {201-16},
	abstract = {We describe a convenient method for constructing new plasmids that relies on interchanging parts of plasmids by homologous recombination in Saccharomyces cerevisiae. A circular recombinant plasmid of a desired structure is regenerated after transformation of yeast with a linearized plasmid and a DNA restriction fragment containing appropriate homology to serve as a substrate for recombinational repair. The free ends of the input DNA molecules need not be homologous in order for efficient recombination between internal homologous regions to occur. The method is particularly useful for incorporating into or removing from plasmids selectable markers, centromere or replication elements, or particular alleles of a gene of interest. Plasmids constructed in yeast can subsequently be recovered in an Escherichia coli host. Using this method, we have constructed an extended series of new yeast centromere, episomal and replicating (YCp, YEp, and YRp) plasmids containing, in various combinations, the selectable yeast markers LEU2, HIS3, LYS2, URA3 and TRP1.
},
	author = {Ma, H and Kunes, S and Schatz, P J and Botstein, D}
}
@article {5618,
	title = {Transformation of yeast with linearized plasmid DNA. Formation of inverted dimers and recombinant plasmid products.},
	journal = {Journal of molecular biology},
	volume = {184},
	number = {3},
	year = {1985},
	note = {n/a
},
	month = {1985 Aug 5},
	pages = {375-87},
	abstract = {The molecular products of DNA double strand break repair were investigated after transformation of yeast (Saccharomyces cerevisiae) with linearized plasmid DNA. DNA of an autonomous yeast plasmid cleaved to generate free ends lacking homology with the yeast genome, when used in transformation along with sonicated non-homologous carrier DNA, gave rise to transformants with high frequency. Most of these transformants were found to harbor a head-to-head (inverted) dimer of the linearized plasmid. This outcome of transformation contrasts with that observed when the carrier DNA is not present. Transformants occur at a much reduced frequency and harbor either the parent plasmid or a plasmid with deletion at the site of the cleavage. When the linearized plasmid is introduced along with sonicated carrier DNA and a homologous DNA restriction fragment that spans the site of plasmid cleavage, homologous recombination restores the plasmid to its original circular form. Inverted dimer plasmids are not detected. This relationship between homologous recombination and a novel DNA transaction that yields rearrangement could be important to the cell, as the latter could lead to a loss of gene function and lethality.
},
	author = {Kunes, S and Botstein, D and Fox, M S}
}
@article {5619,
	title = {Formation of inverted dimer plasmids after transformation of yeast with linearized plasmid DNA.},
	journal = {Cold Spring Harbor symposia on quantitative biology},
	volume = {49},
	year = {1984},
	note = {n/a
},
	month = {1984},
	pages = {617-28},
	abstract = {The formation of an inverted dimer plasmid on transformation with linear molecules is formally analogous to the fusion of the daughters of a broken chromosome at their broken ends. In the latter case, this leads to the formation of a dicentric chromosome, which could break at anaphase. Hence the process is cyclic. Similarly, when our linear molecules are modified by the addition of a cloned yeast centromere, dicentric inverted dimers are not obtained. Instead, we obtain monocentric plasmids with partial duplication and deletion that apparently derive from a process of fusion, bridge-breakage, and fusion. This is not surprising, since it is known that dicentric plasmids undergo breakage in yeast (Mann and Davis 1983). However, any apparent similarity of this process to that which occurs with a broken chromosome in maize must be tempered by the special nature of the transformation process. Most significantly, inverted dimers are rare when sonicated carrier DNA is not present during the transformation. This requirement is not understood, but it is a condition that may not be met in a yeast cell harboring a broken chromosome. It is possible that carrier DNA induces a repair process that results in fusion. On the other hand, a property of the transformation process that results in an inhibition of fusion may be overcome by the presence of carrier DNA. Most inverted dimers are apparently formed from an interaction between two input linear molecules. We cannot rule out the possibility that a minor fraction derive from a single molecule. Thus, the fusion of two input molecules is a much more efficient process than a replicative process that could occur with single linear molecule. For a similar fusion process to occur with a broken yeast chromosome, replication would be required. We do not know if a broken yeast chromosome can replicate. Evidence consistent with the presence of a breakage-fusion-bridge process in yeast has been obtained through the formation of dicentric chromosomes via meiotic recombination (Haber et al. 1984). Spores from these meioses sometimes give rise to a clone that is mixed for markers of the chromosome that could have been dicentric. A process of fusion-bridge-breakage could account for the formation of some of these mixed clones. However, the dicentric chromosomes apparently often survive meiotic disjunction and break in the spore{\textquoteright}s first mitotic anaphase or possibly in a later generation. Thus, the interpretation of the origin of these mixed clones is uncertain. Some aspects of the fusion process are especially intriguing.(ABSTRACT TRUNCATED AT 400 WORDS)
},
	author = {Kunes, S and Botstein, D and Fox, M S}
}
@article {5620,
	title = {Structure of chi hotspots of generalized recombination.},
	journal = {Cell},
	volume = {24},
	number = {2},
	year = {1981},
	note = {n/a
},
	month = {1981 May},
	pages = {429-36},
	abstract = {Chi recombinational hotspots are sites around which the rate of Rec-promoted recombination in bacteriophage lambda is elevated. Examination of a derivative of lambda into which the plasmid pBR322 was inserted reveals that pBR322 lacks Chi sites. Using this lambda-pBR322 hybrid, we obtained mutations creating Chi sites at three widely separated loci within pBR322. Nucleotide sequence analysis reveals that the mutations are single base-pair changes creating the octamer 5{\textquoteright} GCTGGTGG 3{\textquoteright}. This sequence is present at three previously analyzed Chi sites in lambda, and all analyzed mutations creating or inactivating these Chi sites occur within this octamer. We conclude that Chi is 5{\textquoteright} GCTGGTGG 3{\textquoteright}, or its complement, or both.
},
	author = {Smith, G R and Kunes, S M and Schultz, D W and A. Taylor and Triman, K L}
}
