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4106 Publications

Showing 291-300 of 4106 results
06/27/19 | A split fluorescent reporter with rapid and reversible complementation.
Tebo AG, Gautier A
Nature communications. 06/2019;10:2822. doi: 10.1038/s41467-019-10855-0

Interactions between proteins play an essential role in metabolic and signaling pathways, cellular processes and organismal systems. We report the development of splitFAST, a fluorescence complementation system for the visualization of transient protein-protein interactions in living cells. Engineered from the fluorogenic reporter FAST (Fluorescence-Activating and absorption-Shifting Tag), which specifically and reversibly binds fluorogenic hydroxybenzylidene rhodanine (HBR) analogs, splitFAST displays rapid and reversible complementation, allowing the real-time visualization of both the formation and the dissociation of a protein assembly.

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01/10/24 | A split-GAL4 driver line resource for Drosophila CNS cell types
Geoffrey W Meissner , Allison Vannan , Jennifer Jeter , Kari Close , Gina M DePasquale , Zachary Dorman , Kaitlyn Forster , Jaye Anne Beringer , Theresa V Gibney , Joanna H Hausenfluck , Yisheng He , Kristin Henderson , Lauren Johnson , Rebecca M Johnston , Gudrun Ihrke , Nirmala Iyer , Rachel Lazarus , Kelley Lee , Hsing-Hsi Li , Hua-Peng Liaw , Brian Melton , Scott Miller , Reeham Motaher , Alexandra Novak , Omotara Ogundeyi , Alyson Petruncio , Jacquelyn Price , Sophia Protopapas , Susana Tae , Jennifer Taylor , Rebecca Vorimo , Brianna Yarbrough , Kevin Xiankun Zeng , Christopher T Zugates , Heather Dionne , Claire Angstadt , Kelly Ashley , Amanda Cavallaro , Tam Dang , Guillermo A Gonzalez III , Karen L Hibbard , Cuizhen Huang , Jui-Chun Kao , Todd Laverty , Monti Mercer , Brenda Perez , Scarlett Pitts , Danielle Ruiz , Viruthika Vallanadu , Grace Zhiyu Zheng , Cristian Goina , Hideo Otsuna , Konrad Rokicki , Robert R Svirskas , Han SJ Cheong , Michael-John Dolan , Erica Ehrhardt , Kai Feng , Basel El Galfi , Jens Goldammer , Stephen J Huston , Nan Hu , Masayoshi Ito , Claire McKellar , Ryo Minegishi , Shigehiro Namiki , Aljoscha Nern , Catherine E Schretter , Gabriella R Sterne , Lalanti Venkatasubramanian , Kaiyu Wang , Tanya Wolff , Ming Wu , Reed George , Oz Malkesman , Yoshinori Aso , Gwyneth M Card , Barry J Dickson , Wyatt Korff , Kei Ito , James W Truman , Marta Zlatic , Gerald M Rubin , FlyLight Project Team
bioRxiv. 2024 Jan 10:. doi: 10.1101/2024.01.09.574419

Techniques that enable precise manipulations of subsets of neurons in the fly central nervous system have greatly facilitated our understanding of the neural basis of behavior. Split-GAL4 driver lines allow specific targeting of cell types in Drosophila melanogaster and other species. We describe here a collection of 3060 lines targeting a range of cell types in the adult Drosophila central nervous system and 1373 lines characterized in third-instar larvae. These tools enable functional, transcriptomic, and proteomic studies based on precise anatomical targeting. NeuronBridge and other search tools relate light microscopy images of these split-GAL4 lines to connectomes reconstructed from electron microscopy images. The collections are the result of screening over 77,000 split hemidriver combinations. In addition to images and fly stocks for these well-characterized lines, we make available 300,000 new 3D images of other split-GAL4 lines.

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01/06/25 | A split-GAL4 driver line resource for Drosophila neuron types
Meissner GW, Vannan A, Jeter J, Close K, Depasquale GM, Dorman Z, Forster K, Beringer JA, Gibney TV, Hausenfluck JH, He Y, Henderson K, Johnson L, Johnston RM, Ihrke G, Iyer N, Lazarus R, Lee K, Li H, Liaw H, Melton B, Miller S, Motaher R, Novak A, Ogundeyi O, Petruncio A, Price J, Protopapas S, Tae S, Taylor J, Vorimo R, Yarbrough B, Zeng KX, Zugates CT, Dionne H, Angstadt C, Ashley K, Cavallaro A, Dang T, Gonzalez GA, Hibbard KL, Huang C, Kao J, Laverty T, Mercer M, Perez B, Pitts S, Ruiz D, Vallanadu V, Zheng GZ, Goina C, Otsuna H, Rokicki K, Svirskas RR, Cheong HS, Dolan M, Ehrhardt E, Feng K, El Galfi B, Goldammer J, Huston SJ, Hu N, Ito M, McKellar C, minegishi r, Namiki S, Nern A, Schretter CE, Sterne GR, Venkatasubramanian L, Wang K, Wolff T, Wu M, George R, Malkesman O, Aso Y, Card GM, Dickson BJ, Korff W, Ito K, Truman JW, Zlatic M, Rubin GM
Spruston LabMenon Lab
09/29/09 | A state-mutating genetic algorithm to design ion-channel models.
Menon V, Spruston N, Kath WL
Proceedings of the National Academy of Sciences of the United States of America. 2009 Sep 29;106(39):16829-34. doi: 10.1073/pnas.0903766106

Realistic computational models of single neurons require component ion channels that reproduce experimental findings. Here, a topology-mutating genetic algorithm that searches for the best state diagram and transition-rate parameters to model macroscopic ion-channel behavior is described. Important features of the algorithm include a topology-altering strategy, automatic satisfaction of equilibrium constraints (microscopic reversibility), and multiple-protocol fitting using sequential goal programming rather than explicit weighting. Application of this genetic algorithm to design a sodium-channel model exhibiting both fast and prolonged inactivation yields a six-state model that produces realistic activity-dependent attenuation of action-potential backpropagation in current-clamp simulations of a CA1 pyramidal neuron.

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01/01/17 | A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs.
Rivas E, Clements J, Eddy SR
Nature Methods. 2017 Jan 31;14(1):45-8

Many functional RNAs have an evolutionarily conserved secondary structure. Conservation of RNA base pairing induces pairwise covariations in sequence alignments. We developed a computational method, R-scape (RNA Structural Covariation Above Phylogenetic Expectation), that quantitatively tests whether covariation analysis supports the presence of a conserved RNA secondary structure. R-scape analysis finds no statistically significant support for proposed secondary structures of the long noncoding RNAs HOTAIR, SRA, and Xist.

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11/15/02 | A stimulus generating system for studying wind sensation in the American cockroach.
Rinberg D, Davidowitz H
Journal of Neuroscience Methods. 2002 Nov 15;121(1):1-11. doi: 10.1523/JNEUROSCI.3613-08.2008

A novel system for the generation and measurement of a two dimensional wind stimulus is proposed and described. This system was used to investigate the wind sensation of the American cockroach. The new aspects of this system are (a) a pair of computer driven wind tunnels that are shown to produce non-turbulent flows and (b) a novel fiber optic wind detector that measures both amplitude and direction of the wind. Winds can be produced and measured in behaviorally relevant frequency and amplitude ranges without perturbing the airflow. The combination of both the wind generation system and wind detector makes the system very flexible and allows the generation of stimuli with any given spectrum. The two dimensional wind stimulus is shown to be very reproducible. The wind detector is independent of the wind generation system so it can be used for measuring natural winds as well. Experimental data obtained on the cockroach are presented.

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01/03/11 | A structural and functional ground plan for neurons in the hindbrain of zebrafish
Amina Kinkhabwala , Michael Riley , Minoru Koyama , Joost Monen , Chie Satou , Yukiko Kimura , Shin-ichi Higashijima , Joseph Fetcho
Proceedings of the National Academy of Sciences. 01/2011;108:1164-1169. doi: 10.1073/pnas.1012185108

The vertebrate hindbrain contains various sensory-motor networks controlling movements of the eyes, jaw, head, and body. Here we show that stripes of neurons with shared neurotransmitter phenotype that extend throughout the hindbrain of young zebrafish reflect a broad underlying structural and functional patterning. The neurotransmitter stripes contain cell types with shared gross morphologies and transcription factor markers. Neurons within a stripe are stacked systematically by extent and location of axonal projections, input resistance, and age, and are recruited along the axis of the stripe during behavior. The implication of this pattern is that the many networks in hindbrain are constructed from a series of neuronal components organized into stripes that are ordered from top to bottom according to a neuron's age, structural and functional properties, and behavioral roles. This simple organization probably forms a foundation for the construction of the networks underlying the many behaviors produced by the hindbrain.

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01/18/11 | A structural and functional ground plan for neurons in the hindbrain of zebrafish.
Kinkhabwala A, Riley M, Koyama M, Monen J, Satou C, Kimura Y, Higashijima S, Fetcho J
Proceedings of the National Academy of Sciences of the United States of America. 2011 Jan 18;108(3):1164-9. doi: 10.1073/pnas.1012185108

The vertebrate hindbrain contains various sensory-motor networks controlling movements of the eyes, jaw, head, and body. Here we show that stripes of neurons with shared neurotransmitter phenotype that extend throughout the hindbrain of young zebrafish reflect a broad underlying structural and functional patterning. The neurotransmitter stripes contain cell types with shared gross morphologies and transcription factor markers. Neurons within a stripe are stacked systematically by extent and location of axonal projections, input resistance, and age, and are recruited along the axis of the stripe during behavior. The implication of this pattern is that the many networks in hindbrain are constructed from a series of neuronal components organized into stripes that are ordered from top to bottom according to a neuron’s age, structural and functional properties, and behavioral roles. This simple organization probably forms a foundation for the construction of the networks underlying the many behaviors produced by the hindbrain.

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11/01/94 | A sublinear algorithm for approximate keyword matching.
Myers E
Algorithmica. 1994 Nov;12(4-5):345-74

Given a relatively short query stringW of lengthP, a long subject stringA of lengthN, and a thresholdD, theapproximate keyword search problem is to find all substrings ofA that align withW with not more than D insertions, deletions, and mismatches. In typical applications, such as searching a DNA sequence database, the size of the “database”A is much larger than that of the queryW, e.g.,N is on the order of millions or billions andP is a hundred to a thousand. In this paper we present an algorithm that given a precomputedindex of the databaseA, finds rare matches in time that issublinear inN, i.e.,N c for somec<1. The sequenceA must be overa. finite alphabet σ. More precisely, our algorithm requires 0(DN pow(ɛ)  logN) expected-time where ɛ=D/P is the maximum number of differences as a percentage of query length, and pow(ɛ) is an increasing and concave function that is 0 when ɛ=0. Thus the algorithm is superior to current O(DN) algorithms when ɛ is small enough to guarantee that pow(ɛ) < 1. As seen in the paper, this is true for a wide range of ɛ, e.g., ɛ. up to 33% for DNA sequences (¦⌆¦=4) and 56% for proteins sequences (¦⌆¦=20). In preliminary practical experiments, the approach gives a 50-to 500-fold improvement over previous algorithms for prolems of interest in molecular biology.

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08/23/12 | A subset of dopamine neurons signals reward for odour memory in Drosophila.
Liu C, Placais P, Yamagata N, Pfeiffer BD, Aso Y, Friedrich AB, Siwanowicz I, Rubin GM, Preat T, Tanimoto H
Nature. 2012 Aug 23;488(7412):512-6. doi: 10.1038/nature11304

Animals approach stimuli that predict a pleasant outcome. After the paired presentation of an odour and a reward, Drosophila melanogaster can develop a conditioned approach towards that odour. Despite recent advances in understanding the neural circuits for associative memory and appetitive motivation, the cellular mechanisms for reward processing in the fly brain are unknown. Here we show that a group of dopamine neurons in the protocerebral anterior medial (PAM) cluster signals sugar reward by transient activation and inactivation of target neurons in intact behaving flies. These dopamine neurons are selectively required for the reinforcing property of, but not a reflexive response to, the sugar stimulus. In vivo calcium imaging revealed that these neurons are activated by sugar ingestion and the activation is increased on starvation. The output sites of the PAM neurons are mainly localized to the medial lobes of the mushroom bodies (MBs), where appetitive olfactory associative memory is formed. We therefore propose that the PAM cluster neurons endow a positive predictive value to the odour in the MBs. Dopamine in insects is known to mediate aversive reinforcement signals. Our results highlight the cellular specificity underlying the various roles of dopamine and the importance of spatially segregated local circuits within the MBs.

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