@article {70122, title = {GABAergic neuronal dysfunction underlies tremor in a Drosophila model of Spinocerebellar ataxia 3}, journal = {Dis Model Mech}, year = {2025}, month = {2025 Sep 18}, abstract = {

Tremor is a common movement disorder associated with several neurodegenerative diseases, yet its mechanisms are not well understood. Using a machine learning method, FLLIT, we previously characterised gait and tremor signatures in the Drosophila model for Spinocerebellar ataxia 3 (SCA3), and found them to be analogous to human SCA3. Here, we carried out a functional screen for neuronal populations that underlie tremor, and found that dysfunction of a specific population of neurons in the ventral nerve cord (VNC) is necessary and sufficient for tremor. Adult-onset expression of mutant ATXN3 in or genetic hypo-activation of these neurons leads to tremor, indicating their important role in adult motor control. RNAseq and functional experiments showed that dysfunction of GABAergic neurons, and not other neurotransmitter populations tested, causes tremor. Finally, we identified a small subset of approximately 30 predominantly GABAergic neurons within the adult VNC that are essential for smooth walking. This study demonstrates that tremor in SCA3 flies arises from GABAergic dysfunction, and that FLLIT can be used to dissect motor control mechanisms.

}, issn = {1754-8411}, doi = {10.1242/dmm.052329}, url = {https://doi.org/10.1242/dmm.052329}, author = {Banerjee, Animesh and Chatterjee, Moumita and Tan, Kah Junn and Tay, Shermaine and Duan, Kaibo and Andiappan, Anand Kumar and Howland, Shanshan Wu and Aso, Yoshinori and Aw, Sherry Shiying} } @article {70007, title = {A genetic driver of epileptic encephalopathy impairs gating of synaptic glycolysis}, journal = {bioRxiv}, year = {2025}, month = {2025 Jun 19}, abstract = {

The brain is a disproportionately large consumer of fuel, estimated to expend \~20\% of the whole-body energy budget, and therefore it is critical to adequately control brain fuel expenditures while satisfying its on-demand needs for continued function. The brain is also metabolically vulnerable as the inability to adequately fuel cellular processes that support information transfer between cells leads to rapid neurological impairment. We show here that a genetic driver of early onset epileptic encephalopathy (EOEE), SLC13A5, a Na+/citrate cotransporter (NaCT), is critical for gating the activation of local presynaptic glycolysis. We show that SLC13A5 is in part localized to a presynaptic pool of membrane-bound organelles and acts to transiently clear axonal citrate during electrical activity, in turn activating phosphofructokinase 1. We show that loss of SLC13A5 or mistargeting to the plasma membrane results in suppressed glycolytic gating, activity dependent presynaptic bioenergetic deficits and synapse dysfunction.

}, doi = {10.1101/2025.06.17.660213}, url = {https://www.biorxiv.org/content/early/2025/06/19/2025.06.17.660213}, author = {Koshenov, Zhanat and Kokotos, Alexandros C. and Benedetti, Lorena and Schwartz, Jennifer Lippincott and Ryan, Timothy A.} } @article {69833, title = {Glutamate indicators with increased sensitivity and tailored deactivation rates}, journal = {Nat Methods}, year = {2025}, month = {2025 Dec 23}, abstract = {

Understanding how neurons integrate signals from thousands of input synapses requires methods to monitor neurotransmission across many sites simultaneously. The fluorescent protein glutamate indicator iGluSnFR enables visualization of synaptic signaling, but the sensitivity, scale and speed of such measurements are limited by existing variants. Here we developed two highly sensitive fourth-generation iGluSnFR variants with fast activation and tailored deactivation rates: iGluSnFR4f for tracking rapid dynamics, and iGluSnFR4s for recording from large populations of synapses. These indicators detect glutamate with high spatial specificity and single-vesicle sensitivity in vivo. We used them to record natural patterns of synaptic transmission across multiple experimental contexts in mice, including two-photon imaging in cortical layers 1{\textendash}4 and hippocampal CA1, and photometry in the midbrain. The iGluSnFR4 variants extend the speed, sensitivity and scalability of glutamate imaging, enabling direct observation of information flow through neural networks in the intact brain.

}, doi = {10.1038/s41592-025-02965-z}, url = {https://doi.org/10.1038/s41592-025-02965-z}, author = {Aggarwal, Abhi and Negrean, Adrian and Chen, Yang and Iyer, Rishyashring and Reep, Daniel and Liu, Anyi and Palutla, Anirudh and Xie, Michael E. and MacLennan, Bryan J. and Hagihara, Kenta M. and Kinsey, Lucas W. and Sun, Julianna L. and Yao, Pantong and Zheng, Jihong and Tsang, Arthur and Tsegaye, Getahun and Zhang, Yonghai and Patel, Ronak H. and Arthur, Benjamin J. and Hiblot, Julien and Leippe, Philipp and Tarnawski, Miroslaw and Marvin, Jonathan S. and Vevea, Jason D. and Turaga, Srinivas C. and Tebo, Alison G. and Carandini, Matteo and Rossi, L. F. and Kleinfeld, David and Konnerth, Arthur and Svoboda, Karel and Turner, Glenn C. and Hasseman, Jeremy and Podgorski, Kaspar} } @article {69856, title = {Glutamate indicators with increased sensitivity and tailored deactivation rates}, journal = {Research Square}, year = {2025}, month = {2025 Apr 8}, abstract = {

Identifying the input-output operations of neurons requires measurements of synaptic transmission simultaneously at many of a neuron{\textquoteright}s thousands of inputs in the intact brain. To facilitate this goal, we engineered and screened 3365 variants of the fluorescent protein glutamate indicator iGluSnFR3 in neuron culture, and selected variants in the mouse visual cortex. Two variants have high sensitivity, fast activation (\< 2 ms) and deactivation times tailored for recording large populations of synapses (iGluSnFR4s, 153 ms) or rapid dynamics (iGluSnFR4f, 26 ms). By imaging action-potential evoked signals on axons and visually-evoked signals on dendritic spines, we show that iGluSnFR4s/4f primarily detect local synaptic glutamate with single-vesicle sensitivity. The indicators detect a wide range of naturalistic synaptic transmission, including in the vibrissal cortex layer 4 and in hippocampal CA1 dendrites. iGluSnFR4 increases the sensitivity and scale (4s) or speed (4f) of tracking information flow in neural networks in vivo.

}, doi = {10.21203/rs.3.rs-6257403/v1}, url = {https://doi.org/10.21203/rs.3.rs-6257403/v1}, author = {Podgorski, Kaspar and Aggarwal, Abhi and Negrean, Adrian and Chen, Yang and Iyer, Rishyashring and Reep, Daniel and Liu, Anyi and Palutla, Anirudh and Xie, Michael and Maclennan, Bryan and Hagihara, Kenta and Kinsey, Lucas and Sun, Julianna and Yao, Pantong and Zheng, Jihong and Tsang, Arthur and Tsegaye, Getahun and Zhang, Yonghai and Patel, Ronak and Hasseman, Jeremy} } @article {69678, title = {Genomes of two invasive Adelges species (hemlock woolly adelgid and pineapple gall adelgid) enable characterization of nicotinic acetylcholine receptors}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 26}, abstract = {

Two invasive hemipteran adelgids cause widespread damage to North American conifers. Adelges tsugae (the hemlock woolly adelgid) has decimated Tsuga canadensis and Tsuga caroliniana (the Eastern and Carolina hemlocks, respectively). A. tsugae was introduced from East Asia and reproduces parthenogenetically in North America, where it can kill trees rapidly. A. abietis, introduced from Europe, makes pineapple galls on several North American spruce species, and weakens trees, increasing their susceptibility to other stresses. Broad-spectrum insecticides that are often used to control adelgid populations can have off-target impacts on beneficial insects and the development of more selective chemical treatments could improve control methods and minimize ecological damage. Whole genome sequencing was performed on both species to aid in development of targeted pest control solutions and improve species conservation. The assembled A. tsugae and A. abietis genomes are 231.71 Mbp and 290.39 Mbp, respectively, each consisting of nine chromosomes and both genomes are over 96\% complete based on BUSCO assessment. Genome annotation identified 11,424 and 14,118 protein-coding genes in A. tsugae and A. abietis, respectively. Comparative analysis across 29 Hemipteran species and 14 arthropod outgroups identified 31,666 putative gene families. Gene family expansions in A. abietis included ABC transporters and carboxypeptidases involved in carbohydrate metabolism, while both species showed contractions in core histone families and oxidoreductase pathways. Gene family expansions in A. tsugae highlighted families associated with the regulation of cell differentiation and development (survival motor protein, SMN; juvenile hormone acid methyltransferase JHAMT) as well as those that may be involved in the suppression of plant immunity (clip domain serine protease-D, CLIPD; Endoplasmic reticulum aminopeptidase 1, ERAP1). Among the analyzed gene families, Nicotinic acetylcholine receptors (nAChRs) maintained consistent copy numbers and structural features across species, a finding particularly relevant given their role as targets for current forestry management insecticides. Detailed phylogenetic analysis of nAChR subunits across adelgids and other ecologically important insects revealed remarkable conservation in both sequence composition and predicted structural features, providing crucial insights for the development of more selective pest control strategies.

}, doi = {10.1101/2024.11.21.624573}, url = {https://doi.org/10.1101/2024.11.21.624573}, author = {Glendening, A M and Stephens, Cole and Vuruputoor, Vidya S and Stern, David L and Hogenhout, Saskia A and Mathers, Thomas C and Chaganti, Tesko and Pauloski, Nicole and Cernak, Tim A and Wegrzyn, Jill L and Fetter, Karl C} } @article {69661, title = {GESIAP3.0: Sensor-based Image Analysis Program for Transmission Visualization In Vivo}, journal = {bioRxiv}, year = {2024}, month = {2024 Oct 31}, abstract = {

Synaptic transmission mediated by various neurotransmitters influences a wide range of behaviors. However, understanding how neuromodulatory transmitters encode diverse behaviors and affect their functions remains challenging. Here, we introduce GESIAP3.0, an advanced, third-generation image analysis program based on genetically encoded sensors. This tool enables precise quantitative analysis of transmission in both awake, freely moving animals and immobilized subjects. GESIAP3.0 incorporates movement correction algorithms that effectively eliminate image displacement in behaving animals while optimizing synaptic information extraction and simplifying computations on commodity computers. Quantitative analysis of cholinergic, dopaminergic, and serotonergic transmission, corrected for tissue movement, revealed synaptic properties consistent with measurements from ex vivo wide-field and in vivo two-photon imaging under stable conditions. This validates the applicability of GESIAP3.0 for analyzing synaptic properties of neuromodulatory transmission in behaving animals.

}, doi = {10.1101/2024.10.28.620522}, url = {https://doi.org/10.1101/2024.10.28.620522}, author = {Zhu, Roger E. and Diao, Xintong and Liu, Xiaoyu and Ru, Qin and Wu, Zenan and Zhang, Ziyuan and Looger, Loren L. and Zhu, Jiazhu} } @article {69659, title = {A global dopaminergic learning rate enables adaptive foraging across many options}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 05}, abstract = {

In natural environments, animals must efficiently allocate their choices across multiple concurrently available resources when foraging, a complex decision-making process not fully captured by existing models. To understand how rodents learn to navigate this challenge we developed a novel paradigm in which untrained, water-restricted mice were free to sample from six options rewarded at a range of deterministic intervals and positioned around the walls of a large ( 2m) arena. Mice exhibited rapid learning, matching their choices to integrated reward ratios across six options within the first session. A reinforcement learning model with separate states for staying or leaving an option and a dynamic, global learning rate was able to accurately reproduce mouse learning and decision-making. Fiber photometry recordings revealed that dopamine in the nucleus accumbens core (NAcC), but not dorsomedial striatum (DMS), more closely reflected the global learning rate than local error-based updating. Altogether, our results provide insight into the neural substrate of a learning algorithm that allows mice to rapidly exploit multiple options when foraging in large spatial environments.

}, doi = {10.1101/2024.11.04.621923}, url = {https://doi.org/10.1101/2024.11.04.621923}, author = {Grima, Laura L and Guo, Yipei and Narayan, Lakshmi and Hermundstad, Ann M and Dudman, Joshua T} } @article {69680, title = {Global Neuron Shape Reasoning with Point Affinity Transformers}, journal = {bioRxiv}, year = {2024}, month = {2024 Nov 24}, abstract = {

Connectomics is a subfield of neuroscience that aims to map the brain{\textquoteright}s intricate wiring diagram. Accurate neuron segmentation from microscopy volumes is essential for automating connectome reconstruction. However, current state-of-the-art algorithms use image-based convolutional neural networks that are limited to local neuron shape context. Thus, we introduce a new framework that reasons over global neuron shape with a novel point affinity transformer. Our framework embeds a (multi-)neuron point cloud into a fixed-length feature set from which we can decode any point pair affinities, enabling clustering neuron point clouds for automatic proofreading. We also show that the learned feature set can easily be mapped to a contrastive embedding space that enables neuron type classification using a simple KNN classifier. Our approach excels in two demanding connectomics tasks: proofreading segmentation errors and classifying neuron types. Evaluated on three benchmark datasets derived from state-of-the-art connectomes, our method outperforms point transformers, graph neural networks, and unsupervised clustering baselines.

}, doi = {10.1101/2024.11.24.625067}, url = {https://doi.org/10.1101/2024.11.24.625067}, author = {Troidl, Jakob and Knittel, Johannes and Li, Wanhua and Zhan, Fangneng and Pfister, Hanspeter and Turaga, Srinivas} } @article {68772, title = {Glutamate indicators with improved activation kinetics and localization for imaging synaptic transmission.}, journal = {Nature Methods}, volume = {20}, year = {2023}, month = {2023 Jun 01}, abstract = {

The fluorescent glutamate indicator iGluSnFR enables imaging of neurotransmission with genetic and molecular specificity. However, existing iGluSnFR variants exhibit low in vivo signal-to-noise ratios, saturating activation kinetics and exclusion from postsynaptic densities. Using a multiassay screen in bacteria, soluble protein and cultured neurons, we generated variants with improved signal-to-noise ratios and kinetics. We developed surface display constructs that improve iGluSnFR{\textquoteright}s nanoscopic localization to postsynapses. The resulting indicator iGluSnFR3 exhibits rapid nonsaturating activation kinetics and reports synaptic glutamate release with decreased saturation and increased specificity versus extrasynaptic signals in cultured neurons. Simultaneous imaging and electrophysiology at individual boutons in mouse visual cortex showed that iGluSnFR3 transients report single action potentials with high specificity. In vibrissal sensory cortex layer 4, we used iGluSnFR3 to characterize distinct patterns of touch-evoked feedforward input from thalamocortical boutons and both feedforward and recurrent input onto L4 cortical neuron dendritic spines.

}, issn = {1548-7105}, doi = {10.1038/s41592-023-01863-6}, author = {Aggarwal, Abhi and Liu, Rui and Chen, Yang and Ralowicz, Amelia J and Bergerson, Samuel J and Tomaska, Filip and Mohar, Boaz and Hanson, Timothy L and Hasseman, Jeremy P and Reep, Daniel and Tsegaye, Getahun and Yao, Pantong and Ji, Xiang and Kloos, Marinus and Walpita, Deepika and Patel, Ronak and Mohr, Manuel A and Tillberg, Paul W and Looger, Loren L and Marvin, Jonathan S and Hoppa, Michael B and Konnerth, Arthur and Kleinfeld, David and Schreiter, Eric R and Podgorski, Kaspar} } @article {68068, title = {Gene structure-based homology search identifies highly divergent putative effector gene family.}, journal = {Genome Biology and Evolution}, year = {2022}, month = {2022 May 09}, abstract = {

Homology of highly divergent genes often cannot be determined from sequence similarity alone. For example, we recently identified in the aphid Hormaphis cornu a family of rapidly evolving bicycle genes, which encode novel proteins implicated as plant gall effectors, and sequence similarity search methods yielded few putative bicycle homologs in other species. Coding sequence-independent features of genes, such as intron-exon boundaries, often evolve more slowly than coding sequences, however, and can provide complementary evidence for homology. We found that a linear logistic regression classifier using only structural features of bicycle genes identified many putative bicycle homologs in other species. Independent evidence from sequence features and intron locations supported homology assignments. To test the potential roles of bicycle genes in other aphids, we sequenced the genome of a second gall-forming aphid, Tetraneura nigriabdominalis, and found that many bicycle genes are strongly expressed in the salivary glands of the gall forming foundress. In addition, bicycle genes are strongly overexpressed in the salivary glands of a non-gall forming aphid, Acyrthosiphon pisum, and in the non-gall forming generations of Hormaphis cornu. These observations suggest that Bicycle proteins may be used by multiple aphid species to manipulate plants in diverse ways. Incorporation of gene structural features into sequence search algorithms may aid identification of deeply divergent homologs, especially of rapidly evolving genes involved in host-parasite interactions.

}, issn = {1759-6653}, doi = {10.1093/gbe/evac069}, author = {Stern, David L and Han, Clair} } @article {65808, title = {A geometric framework to predict structure from function in neural networks}, journal = {Physical Review Research}, volume = {4}, year = {2022}, month = {2022 Jun 29}, pages = {023255}, abstract = {

Neural computation in biological and artificial networks relies on nonlinear synaptic integration. The structural connectivity matrix of synaptic weights between neurons is a critical determinant of overall network function. However, quantitative links between neural network structure and function are complex and subtle. For example, many networks can give rise to similar functional responses, and the same network can function differently depending on context. Whether certain patterns of synaptic connectivity are required to generate specific network-level computations is largely unknown. Here we introduce a geometric framework for identifying synaptic connections required by steady-state responses in recurrent networks of rectified-linear neurons. Assuming that the number of specified response patterns does not exceed the number of input synapses, we analytically calculate all feedforward and recurrent connectivity matrices that can generate the specified responses from the network inputs. We then use this analytical characterization to rigorously analyze the solution space geometry and derive certainty conditions guaranteeing a non-zero synapse between neurons. Numerical simulations of feedforward and recurrent networks verify our analytical results. Our theoretical framework could be applied to neural activity data to make anatomical predictions that follow generally from the model architecture. It thus provides novel opportunities for discerning what model features are required to accurately relate neural network structure and function.

}, doi = {10.1103/PhysRevResearch.4.023255}, url = {https://doi.org/10.1103/PhysRevResearch.4.023255}, author = {Biswas, Tirthabir and Fitzgerald, James E} } @article {67244, title = {A general method to improve fluorophores using deuterated auxochromes.}, journal = {JACS Au}, volume = {1}, year = {2021}, month = {2021 May 24}, pages = {690-6}, abstract = {

Fluorescence microscopy relies on dyes that absorb and then emit photons. In addition to fluorescence, fluorophores can undergo photochemical processes that decrease quantum yield or result in spectral shifts and irreversible photobleaching. Chemical strategies that suppress these undesirable pathways{\textemdash}thereby increasing the brightness and photostability of fluorophores{\textemdash}are crucial for advancing the frontier of bioimaging. Here, we describe a general method to improve small-molecule fluorophores by incorporating deuterium into the alkylamino auxochromes of rhodamines and other dyes. This strategy increases fluorescence quantum yield, inhibits photochemically induced spectral shifts, and slows irreparable photobleaching, yielding next-generation labels with improved performance in cellular imaging experiments.

}, issn = {2691-3704}, doi = {10.1021/jacsau.1c00006}, url = {https://doi.org/10.1021/jacsau.1c00006}, author = {Grimm, Jonathan B. and Xie, Liangqi and Casler, Jason C. and Patel, Ronak and Tkachuk, Ariana N. and Falco, Natalie and Choi, Heejun and Lippincott-Schwartz, Jennifer and Brown, Timothy A. and Glick, Benjamin S. and Liu, Zhe and Lavis, Luke D.} } @article {67712, title = {A genetic screen for Drosophila social isolation mutants and analysis of sex pistol.}, journal = {Scientific Reports}, volume = {11}, year = {2021}, month = {2021 Aug 30}, pages = {17395}, abstract = {

Prolonged periods of forced social isolation is detrimental to well-being, yet we know little about which genes regulate susceptibility to its effects. In the fruit fly, Drosophila melanogaster, social isolation induces stark changes in behavior including increased aggression, locomotor activity, and resistance to ethanol sedation. To identify genes regulating sensitivity to isolation, I screened a collection of sixteen hundred P-element insertion lines for mutants with abnormal levels of all three isolation-induced behaviors. The screen identified three mutants whose affected genes are likely central to regulating the effects of isolation in flies. One mutant, sex pistol (sxp), became extremely aggressive and resistant to ethanol sedation when socially isolated. sxp also had a high level of male-male courtship. The mutation in sxp reduced the expression of two minor isoforms of the actin regulator hts (adducin), as well as mildly reducing expression of CalpA, a calcium-dependent protease. As a consequence, sxp also had increased expression of the insulin-like peptide, dILP5. Analysis of the social behavior of sxp suggests that these minor hts isoforms function to limit isolation-induced aggression, while chronically high levels of dILP5 increase male-male courtship.

}, issn = {2045-2322}, doi = {10.1038/s41598-021-96871-x}, author = {Eddison, Mark} } @article {67821, title = {A genetically defined insula-brainstem circuit selectively controls motivational vigor.}, journal = {Cell}, year = {2021}, month = {2021 Dec 07}, abstract = {

The anterior insular cortex (aIC) plays a critical role in cognitive and motivational control of behavior, but the underlying neural mechanism remains elusive. Here, we show that aIC neurons expressing Fezf2 (aIC), which are the pyramidal tract neurons, signal motivational vigor and invigorate need-seeking behavior through projections to the brainstem nucleus tractus solitarii (NTS). aIC neurons and their postsynaptic NTS neurons acquire anticipatory activity through learning, which encodes the perceived value and the vigor of actions to pursue homeostatic needs. Correspondingly, aIC {\textrightarrow} NTS circuit activity controls vigor, effort, and striatal dopamine release but only if the action is learned and the outcome is needed. Notably, aIC neurons do not represent taste or valence. Moreover, aIC {\textrightarrow} NTS activity neither drives reinforcement nor influences total consumption. These results pinpoint specific functions of aIC {\textrightarrow} NTS circuit for selectively controlling motivational vigor and suggest that motivation is subserved, in part, by aIC{\textquoteright}s top-down regulation of dopamine signaling.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2021.11.019}, author = {Deng, Hanfei and Xiao, Xiong and Yang, Tao and Ritola, Kimberly and Hantman, Adam and Li, Yulong and Huang, Z Josh and Li, Bo} } @article {67816, title = {A genetically encoded fluorescent biosensor for extracellular L-lactate.}, journal = {Nature Communications}, volume = {12}, year = {2021}, month = {2021 Dec 06}, pages = {7058}, abstract = {

L-Lactate, traditionally considered a metabolic waste product, is increasingly recognized as an important intercellular energy currency in mammals. To enable investigations of the emerging roles of intercellular shuttling of L-lactate, we now report an intensiometric green fluorescent genetically encoded biosensor for extracellular L-lactate. This biosensor, designated eLACCO1.1, enables cellular resolution imaging of extracellular L-lactate in cultured mammalian cells and brain tissue.

}, issn = {2041-1723}, doi = {10.1038/s41467-021-27332-2}, author = {Nasu, Yusuke and Murphy-Royal, Ciaran and Wen, Yurong and Haidey, Jordan N and Molina, Rosana S and Abhi Aggarwal and Zhang, Shuce and Kamijo, Yuki and Paquet, Marie-Eve and Podgorski, Kaspar and Drobizhev, Mikhail and Bains, Jaideep S and Lemieux, M Joanne and Gordon, Grant R and Campbell, Robert E} } @article {67765, title = {Genetically identified amygdala-striatal circuits for valence-specific behaviors.}, journal = {Nature Neuroscience}, volume = {24}, year = {2021}, month = {2021 Oct 18}, pages = {1586-1600}, abstract = {

The basolateral amygdala (BLA) plays essential roles in behaviors motivated by stimuli with either positive or negative valence, but how it processes motivationally opposing information and participates in establishing valence-specific behaviors remains unclear. Here, by targeting Fezf2-expressing neurons in the BLA, we identify and characterize two functionally distinct classes in behaving mice, the negative-valence neurons and positive-valence neurons, which innately represent aversive and rewarding stimuli, respectively, and through learning acquire predictive responses that are essential for punishment avoidance or reward seeking. Notably, these two classes of neurons receive inputs from separate sets of sensory and limbic areas, and convey punishment and reward information through projections to the nucleus accumbens and olfactory tubercle, respectively, to drive negative and positive reinforcement. Thus, valence-specific BLA neurons are wired with distinctive input-output structures, forming a circuit framework that supports the roles of the BLA in encoding, learning and executing valence-specific motivated behaviors.

}, issn = {1546-1726}, doi = {10.1038/s41593-021-00927-0}, author = {Zhang, Xian and Guan, Wuqiang and Yang, Tao and Furlan, Alessandro and Xiao, Xiong and Yu, Kai and An, Xu and Galbavy, William and Ramakrishnan, Charu and Deisseroth, Karl and Ritola, Kimberly and Hantman, Adam and He, Miao and Josh Huang, Z and Li, Bo} } @article {67200, title = {A guide to accurate reporting in digital image processing - can anyone reproduce your quantitative analysis?}, journal = {Journal of Cell Science}, volume = {134}, year = {2021}, month = {2021 Mar 30}, abstract = {

Considerable attention has been recently paid to improving replicability and reproducibility in life science research. This has resulted in commendable efforts to standardize a variety of reagents, assays, cell lines and other resources. However, given that microscopy is a dominant tool for biologists, comparatively little discussion has been offered regarding how the proper reporting and documentation of microscopy relevant details should be handled. Image processing is a critical step of almost any microscopy-based experiment; however, improper, or incomplete reporting of its use in the literature is pervasive. The chosen details of an image processing workflow can dramatically determine the outcome of subsequent analyses, and indeed, the overall conclusions of a study. This Review aims to illustrate how proper reporting of image processing methodology improves scientific reproducibility and strengthens the biological conclusions derived from the results.

}, issn = {1477-9137}, doi = {10.1242/jcs.254151}, author = {Aaron, Jesse and Chew, Teng-Leong} } @article {65582, title = {Gene expression analysis in the mouse brainstem identifies Cart and Nesfatin as neuropeptides co-expressed in the Calbindin-positive neurons of the Nucleus papilio.}, journal = {Sleep}, year = {2020}, month = {2020 Apr 28}, abstract = {

The brainstem contains several neuronal populations, heterogeneous in term of neurotransmitter/neuropeptide content, which are important for controlling various aspects of the REM phase of sleep. Among these populations are the Calbindin (Calb)-immunoreactive NPCalb neurons, located in the Nucleus papilio, within the dorsal paragigantocellular nucleus (DPGi), and recently shown to control eye movement during the REM phase of sleep. We performed in depth data-mining of the in-situ hybridization data collected at the Allen Brain Atlas, in order to identify potentially interesting genes expressed in this brainstem nucleus. Our attention focused on genes encoding neuropeptides, including Cart (Cocaine and Amphetamine Regulated Transcripts) and Nesfatin1. While Nesfatin1 appeared ubiquitously expressed in this Calb-positive neuronal population, Cart was co-expressed in only a subset of these glutamatergic NPCalb neurons. Furthermore, a REM sleep deprivation and rebound assay performed with mice revealed that the Cart-positive neuronal population within the DPGi was activated during REM sleep (as measured by c-fos immunoreactivity), suggesting a role of this neuropeptide in regulating some aspects of REM sleep. The assembled information could afford functional clues to investigators, conducive to further experimental pursuits.

}, issn = {1550-9109}, doi = {10.1093/sleep/zsaa085}, author = {Girard, F and von Siebenthal, M and Davis, F P and Celio, M R} } @article {65378, title = {A general approach to engineer positive-going eFRET voltage indicators}, journal = {Nature Communications}, volume = {11}, year = {2020}, month = {2020 Jul 10}, abstract = {

We engineered electrochromic fluorescence resonance energy transfer (eFRET) genetically encoded voltage indicators (GEVIs) with {\textquotedblleft}positive-going{\textquotedblright} fluorescence response to membrane depolarization through rational manipulation of the native proton transport pathway in microbial rhodopsins. We transformed the state-of-the-art eFRET GEVI Voltron into Positron, with kinetics and sensitivity equivalent to Voltron but flipped fluorescence signal polarity. We further applied this general approach to GEVIs containing different voltage sensitive rhodopsin domains and various fluorescent dye and fluorescent protein reporters.

}, author = {Abdelfattah, Ahmed S and Valenti, Rosario and Zheng, Jihong and Wong, Allan and Podgorski, Kaspar and Koyama, Minoru and Kim, Douglas S. and Schreiter, Eric R and Project Team GENIE} } @article {65667, title = {A general method to optimize and functionalize red-shifted rhodamine dyes.}, journal = {Nature Methods}, year = {2020}, month = {2020 Jul 27}, abstract = {

Expanding the palette of fluorescent dyes is vital to push the frontier of biological imaging. Although rhodamine dyes remain the premier type of small-molecule fluorophore owing to their bioavailability and brightness, variants excited with far-red or near-infrared light suffer from poor performance due to their propensity to adopt a lipophilic, nonfluorescent form. We report a framework for rationalizing rhodamine behavior in biological environments and a general chemical modification for rhodamines that optimizes long-wavelength variants and enables facile functionalization with different chemical groups. This strategy yields red-shifted {\textquoteright}Janelia Fluor{\textquoteright} (JF) dyes useful for biological imaging experiments in cells and in vivo.

}, issn = {1548-7105}, doi = {10.1038/s41592-020-0909-6}, author = {Grimm, Jonathan B and Tkachuk, Ariana N and Xie, Liangqi and Choi, Heejun and Mohar, Boaz and Falco, Natalie and Schaefer, Kathy and Patel, Ronak and Zheng, Qinsi and Liu, Zhe and Lippincott-Schwartz, Jennifer and Brown, Timothy A and Lavis, Luke D} } @article {65282, title = {A genetic, genomic, and computational resource for exploring neural circuit function.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Jan 15}, abstract = {

The anatomy of many neural circuits is being characterized with increasing resolution, but their molecular properties remain mostly unknown. Here, we characterize gene expression patterns in distinct neural cell types of the visual system using genetic lines to access individual cell types, the TAPIN-seq method to measure their transcriptomes, and a probabilistic method to interpret these measurements. We used these tools to build a resource of high-resolution transcriptomes for 100 driver lines covering 67 cell types, available at http://www.opticlobe.com. Combining these transcriptomes with recently reported connectomes helps characterize how information is transmitted and processed across a range of scales, from individual synapses to circuit pathways. We describe examples that include identifying neurotransmitters, including cases of apparent co-release, generating functional hypotheses based on receptor expression, as well as identifying strong commonalities between different cell types.

}, issn = {2050-084X}, doi = {10.7554/eLife.50901}, author = {Davis, Fred P and Nern, Aljoscha and Picard, Serge and Reiser, Michael B and Rubin, Gerald M and Eddy, Sean R and Henry, Gilbert L} } @article {65739, title = {A genetically defined compartmentalized striatal direct pathway for negative reinforcement.}, journal = {Cell}, volume = {181}, year = {2020}, month = {2020 Oct 1}, pages = {211}, abstract = {

The striosome compartment within the dorsal striatum has been implicated in reinforcement learning and regulation of motivation, but how striosomal neurons contribute to these functions remains elusive. Here, we show that a genetically identified striosomal population, which expresses the Teashirt family zinc finger 1 (Tshz1) and belongs to the direct pathway, drives negative reinforcement and is essential for aversive learning in mice. Contrasting a "conventional" striosomal direct pathway, the Tshz1 neurons cause aversion, movement suppression, and negative reinforcement once activated, and they receive a distinct set of synaptic inputs. These neurons are predominantly excited by punishment rather than reward and represent the anticipation of punishment or the motivation for avoidance. Furthermore, inhibiting these neurons impairs punishment-based learning without affecting reward learning or movement. These results establish a major role of striosomal neurons in behaviors reinforced by punishment and moreover uncover functions of the direct pathway unaccounted for in classic models.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.08.032}, author = {Xiao, Xiong and Deng, Hanfei and Furlan, Alessandro and Yang, Tao and Zhang, Xian and Hwang, Ga-Ram and Tucciarone, Jason and Wu, Priscilla and He, Miao and Palaniswamy, Ramesh and Ramakrishnan, Charu and Ritola, Kimberly and Hantman, Adam and Deisseroth, Karl and Osten, Pavel and Huang, Z Josh and Li, Bo} } @article {65636, title = {Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.}, journal = {Science Advances}, volume = {6}, year = {2020}, month = {2020 Jun 17}, pages = {eaaz6699}, abstract = {

Transcriptional bursting is the stochastic activation and inactivation of promoters, contributing to cell-to-cell heterogeneity in gene expression. However, the mechanism underlying the regulation of transcriptional bursting kinetics (burst size and frequency) in mammalian cells remains elusive. In this study, we performed single-cell RNA sequencing to analyze the intrinsic noise and mRNA levels for elucidating the transcriptional bursting kinetics in mouse embryonic stem cells. Informatics analyses and functional assays revealed that transcriptional bursting kinetics was regulated by a combination of promoter- and gene body-binding proteins, including the polycomb repressive complex 2 and transcription elongation factors. Furthermore, large-scale CRISPR-Cas9-based screening identified that the Akt/MAPK signaling pathway regulated bursting kinetics by modulating transcription elongation efficiency. These results uncovered the key molecular mechanisms underlying transcriptional bursting and cell-to-cell gene expression noise in mammalian cells.

}, issn = {2375-2548}, doi = {10.1126/sciadv.aaz6699}, author = {Ochiai, Hiroshi and Hayashi, Tetsutaro and Umeda, Mana and Yoshimura, Mika and Harada, Akihito and Shimizu, Yukiko and Nakano, Kenta and Saitoh, Noriko and Liu, Zhe and Yamamoto, Takashi and Okamura, Tadashi and Ohkawa, Yasuyuki and Kimura, Hiroshi and Nikaido, Itoshi} } @article {65657, title = {Growth cone-localized microtubule organizing center establishes microtubule orientation in dendrites.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Jul 13}, abstract = {

A polarized arrangement of neuronal microtubule arrays is the foundation of membrane trafficking and subcellular compartmentalization. Conserved among both invertebrates and vertebrates, axons contain exclusively {\textquoteright}plus-end-out{\textquoteright} microtubules while dendrites contain a high percentage of {\textquoteright}minus-end-out{\textquoteright} microtubules, the origins of which have been a mystery. Here we show that in the dendritic growth cone contains a non-centrosomal microtubule organizing center, which generates minus-end-out microtubules along outgrowing dendrites and plus-end-out microtubules in the growth cone. RAB-11-positive endosomes accumulate in this region and co-migrate with the microtubule nucleation complex γ-TuRC. The MTOC tracks the extending growth cone by kinesin-1/UNC-116-mediated endosome movements on distal plus-end-out microtubules and dynein clusters this advancing MTOC. Critically, perturbation of the function or localization of the MTOC causes reversed microtubule polarity in dendrites. These findings unveil the endosome-localized dendritic MTOC as a critical organelle for establishing axon-dendrite polarity.

}, issn = {2050-084X}, doi = {10.7554/eLife.56547}, author = {Liang, Xing and Kokes, Marcela and Fetter, Richard D and Sallee, Maria Danielle and Moore, Adrian W and Feldman, Jessica L and Shen, Kang} } @article {65224, title = {Gas cluster ion beam SEM for imaging of large tissue samples with 10 nm isotropic resolution.}, journal = {Nature Methods}, volume = {17}, year = {2019}, month = {2020 Jan 01}, pages = {68-71}, abstract = {

We demonstrate gas cluster ion beam scanning electron microscopy (SEM), in which wide-area ion milling is performed on a series of thick tissue sections. This three-dimensional electron microscopy technique acquires datasets with \<10 nm isotropic resolution of each section, and these can then be stitched together to span the sectioned volume. Incorporating gas cluster ion beam SEM into existing single-beam and multibeam SEM workflows should be straightforward, increasing reliability while improving z resolution by a factor of three or more.

}, issn = {1548-7105}, doi = {10.1038/s41592-019-0641-2}, author = {Hayworth, Kenneth J and Peale, David and Januszewski, Micha{\l} and Knott, Graham W and Lu, Zhiyuan and Xu, C Shan and Hess, Harald F} } @article {64823, title = {GCIB-SEM: A path to 10 nm isotropic imaging of cubic millimeter volumes.}, journal = {bioRxiv}, year = {2019}, month = {2019 Feb 28}, abstract = {Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) generates 3D datasets optimally suited for segmentation of cell ultrastructure and automated connectome tracing but is limited to small fields of view and is therefore incompatible with the new generation of ultrafast multibeam SEMs. In contrast, section-based techniques are multibeam-compatible but are limited in z-resolution making automatic segmentation of cellular ultrastructure difficult. Here we demonstrate a novel 3D electron microscopy technique, Gas Cluster Ion Beam SEM (GCIB-SEM), in which top-down, wide-area ion milling is performed on a series of thick sections, acquiring < 10 nm isotropic datasets of each which are then stitched together to span the full sectioned volume. Based on our results, incorporating GCIB-SEM into existing single beam and multibeam SEM workflows should be straightforward and should dramatically increase reliability while simultaneously improving z-resolution by a factor of 3 or more.}, doi = {10.1101/563239}, author = {Hayworth, Kenneth J and Peale, David R and Januszewski, Michal and Knott, Graham and Lu, Zhiyuan and Xu, C. Shan and Hess, Harald F} } @article {65234, title = {Generation of stable heading representations in diverse visual scenes.}, journal = {Nature}, volume = {576}, year = {2019}, month = {2019 Nov 20}, pages = {126-31}, abstract = {

Many animals rely on an internal heading representation when navigating in varied environments. How this representation is linked to the sensory cues that define different surroundings is unclear. In the fly brain, heading is represented by {\textquoteright}compass{\textquoteright} neurons that innervate a ring-shaped structure known as the ellipsoid body. Each compass neuron receives inputs from {\textquoteright}ring{\textquoteright} neurons that are selective for particular visual features; this combination provides an ideal substrate for the extraction of directional information from a visual scene. Here we combine two-photon calcium imaging and optogenetics in tethered flying flies with circuit modelling, and show how the correlated activity of compass and visual neurons drives plasticity, which flexibly transforms two-dimensional visual cues into a stable heading representation. We also describe how this plasticity enables the fly to convert a partial heading representation, established from orienting within part of a novel setting, into a complete heading representation. Our results provide mechanistic insight into the memory-related computations that are essential for flexible navigation in varied surroundings.

}, issn = {1476-4687}, doi = {10.1038/s41586-019-1767-1}, author = {Kim, Sung Soo and Hermundstad, Ann M and Romani, Sandro and Abbott, L F and Jayaraman, Vivek} } @article {65157, title = {Genetic dissection of active forgetting in labile and consolidated memories in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, year = {2019}, month = {2019 Oct 01}, pages = {21191-97}, abstract = {

Different memory components are forgotten through distinct molecular mechanisms. In , the activation of 2 Rho GTPases (Rac1 and Cdc42), respectively, underlies the forgetting of an early labile memory (anesthesia-sensitive memory, ASM) and a form of consolidated memory (anesthesia-resistant memory, ARM). Here, we dissected the molecular mechanisms that tie Rac1 and Cdc42 to the different types of memory forgetting. We found that 2 WASP family proteins, SCAR/WAVE and WASp, act downstream of Rac1 and Cdc42 separately to regulate ASM and ARM forgetting in mushroom body neurons. Arp2/3 complex, which organizes branched actin polymerization, is a canonical downstream effector of WASP family proteins. However, we found that Arp2/3 complex is required in Cdc42/WASp-mediated ARM forgetting but not in Rac1/SCAR-mediated ASM forgetting. Instead, we identified that Rac1/SCAR may function with formin Diaphanous (Dia), a nucleator that facilitates linear actin polymerization, in ASM forgetting. The present study, complementing the previously identified Rac1/cofilin pathway that regulates actin depolymerization, suggests that Rho GTPases regulate forgetting by recruiting both actin polymerization and depolymerization pathways. Moreover, Rac1 and Cdc42 may regulate different types of memory forgetting by tapping into different actin polymerization mechanisms.

}, issn = {1091-6490}, doi = {10.1073/pnas.1903763116}, author = {Gao, Yang and Shuai, Yichun and Zhang, Xuchen and Peng, Yuwei and Wang, Lianzhang and He, Jing and Zhong, Yi and Li, Qian} } @article {68360, title = {Genetic Identification of Vagal Sensory Neurons That Control Feeding}, journal = {Cell}, volume = {179}, year = {2019}, month = {11/2019}, pages = {1129-1143.e23}, abstract = {

Summary Energy homeostasis requires precise measurement of the quantity and quality of ingested food. The vagus nerve innervates the gut and can detect diverse interoceptive cues, but the identity of the key sensory neurons and corresponding signals that regulate food intake remains unknown. Here, we use an approach for target-specific, single-cell RNA sequencing to generate a map of the vagal cell types that innervate the gastrointestinal tract. We show that unique molecular markers identify vagal neurons with distinct innervation patterns, sensory endings, and function. Surprisingly, we find that food intake is most sensitive to stimulation of mechanoreceptors in the intestine, whereas nutrient-activated mucosal afferents have no effect. Peripheral manipulations combined with central recordings reveal that intestinal mechanoreceptors, but not other cell types, potently and durably inhibit hunger-promoting AgRP neurons in the hypothalamus. These findings identify a key role for intestinal mechanoreceptors in the regulation of feeding.

}, keywords = {AgRP Neurons, chemogenetics, fiber photometry, Hypothalamus, Optogenetics, RNA sequencing, Satiation, stretch, vagal afferents, vagus nerve}, issn = {0092-8674}, doi = {https://doi.org/10.1016/j.cell.2019.10.031}, url = {https://www.sciencedirect.com/science/article/pii/S009286741931181X}, author = {Ling Bai and Sheyda Mesgarzadeh and Karthik S. Ramesh and Erica L. Huey and Yin Liu and Lindsay A. Gray and Tara J. Aitken and Yiming Chen and Lisa R. Beutler and Jamie S. Ahn and Linda Madisen and Hongkui Zeng and Mark A. Krasnow and Zachary A. Knight} } @article {65056, title = {A genetically encoded fluorescent sensor for in vivo imaging of GABA.}, journal = {Nature Methods}, volume = {16}, year = {2019}, month = {2019 Jul 15}, pages = {763-770}, abstract = {

Current techniques for monitoring GABA (γ-aminobutyric acid), the primary inhibitory neurotransmitter in vertebrates, cannot follow transients in intact neural circuits. To develop a GABA sensor, we applied the design principles used to create the fluorescent glutamate receptor iGluSnFR. We used a protein derived from a previously unsequenced Pseudomonas fluorescens strain and performed structure-guided mutagenesis and library screening to obtain intensity-based GABA sensing fluorescence reporter (iGABASnFR) variants. iGABASnFR is genetically encoded, detects GABA release evoked by electric stimulation of afferent fibers in acute brain slices and produces readily detectable fluorescence increases in vivo in mice and zebrafish. We applied iGABASnFR to track mitochondrial GABA content and its modulation by an anticonvulsant, swimming-evoked, GABA-mediated transmission in zebrafish cerebellum, GABA release events during interictal spikes and seizures in awake mice, and found that GABA-mediated tone decreases during isoflurane anesthesia.

}, issn = {1548-7105}, doi = {10.1038/s41592-019-0471-2}, author = {Marvin, Jonathan S and Shimoda, Yoshiteru and Magloire, Vincent and Leite, Marco and Kawashima, Takashi and Jensen, Thomas P and Kolb, Ilya and Knott, Erika L and Novak, Ondrej and Podgorski, Kaspar and Leidenheimer, Nancy J and Rusakov, Dmitri A and Ahrens, Misha B and Kullmann, Dimitri M and Looger, Loren L} } @article {56204, title = {A genetically encoded near-infrared fluorescent calcium ion indicator.}, journal = {Nature Methods}, volume = {16}, year = {2019}, month = {2019 Jan 21}, pages = {171-4}, abstract = {

We report an intensiometric, near-infrared fluorescent, genetically encoded calcium ion (Ca) indicator (GECI) with excitation and emission maxima at 678 and 704 nm, respectively. This GECI, designated NIR-GECO1, enables imaging of Ca transients in cultured mammalian cells and brain tissue with sensitivity comparable to that of currently available visible-wavelength GECIs. We demonstrate that NIR-GECO1 opens up new vistas for multicolor Ca imaging in combination with other optogenetic indicators and actuators.

}, issn = {1548-7105}, doi = {10.1038/s41592-018-0294-6}, author = {Qian, Yong and Piatkevich, Kiryl D and Mc Larney, Benedict and Abdelfattah, Ahmed S and Mehta, Sohum and Murdock, Mitchell H and Gottschalk, Sven and Molina, Rosana S and Zhang, Wei and Chen, Yingche and Wu, Jiahui and Drobizhev, Mikhail and Hughes, Thomas E and Zhang, Jin and Schreiter, Eric R and Shoham, Shy and Razansky, Daniel and Boyden, Edward S and Campbell, Robert E} } @article {64796, title = {A genetically encoded single-wavelength sensor for imaging cytosolic and cell surface ATP.}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {2019 Feb 12}, pages = {711}, abstract = {

Adenosine 5{\textquoteright} triphosphate (ATP) is a universal intracellular energy source and an evolutionarily ancient, ubiquitous extracellular signal in diverse species. Here, we report the generation and characterization of single-wavelength genetically encoded fluorescent sensors (iATPSnFRs) for imaging extracellular and cytosolic ATP from insertion of circularly permuted superfolder GFP into the epsilon subunit of FF-ATPase from Bacillus PS3. On the cell surface and within the cytosol, iATPSnFR responds to relevant ATP concentrations (30 μM to 3 mM) with fast increases in fluorescence. iATPSnFRs can be genetically targeted to specific cell types and sub-cellular compartments, imaged with standard light microscopes, do not respond to other nucleotides and nucleosides, and when fused with a red fluorescent protein function as ratiometric indicators. After careful consideration of their modest pH sensitivity, iATPSnFRs represent promising reagents for imaging ATP in the extracellular space and within cells during a variety of settings, and for further application-specific refinements.

}, issn = {2041-1723}, doi = {10.1038/s41467-019-08441-5}, author = {Lobas, Mark A and Tao, Rongkun and Nagai, Jun and Kronschl{\"a}ger, Mira T and Borden, Philip M and Marvin, Jonathan S and Looger, Loren L and Khakh, Baljit S} } @article {65020, title = {Genetics of intellectual disability in consanguineous families.}, journal = {Mol Psychiatry}, volume = {24}, year = {2019}, month = {2018 Jan 04}, pages = {1027-1039}, abstract = {

Autosomal recessive (AR) gene defects are the leading genetic cause of intellectual disability (ID) in countries with frequent parental consanguinity, which account for about 1/7th of the world population. Yet, compared to autosomal dominant de novo mutations, which are the predominant cause of ID in Western countries, the identification of AR-ID genes has lagged behind. Here, we report on whole exome and whole genome sequencing in 404 consanguineous predominantly Iranian families with two or more affected offspring. In 219 of these, we found likely causative variants, involving 77 known and 77 novel AR-ID (candidate) genes, 21 X-linked genes, as well as 9 genes previously implicated in diseases other than ID. This study, the largest of its kind published to date, illustrates that high-throughput DNA sequencing in consanguineous families is a superior strategy for elucidating the thousands of hitherto unknown gene defects underlying AR-ID, and it sheds light on their prevalence.

}, issn = {1476-5578}, doi = {10.1038/s41380-017-0012-2}, author = {Hu, Hao and Kahrizi, Kimia and Musante, Luciana and Fattahi, Zohreh and Herwig, Ralf and Hosseini, Masoumeh and Oppitz, Cornelia and Abedini, Seyedeh Sedigheh and Suckow, Vanessa and Larti, Farzaneh and Beheshtian, Maryam and Lipkowitz, Bettina and Akhtarkhavari, Tara and Mehvari, Sepideh and Otto, Sabine and Mohseni, Marzieh and Arzhangi, Sanaz and Jamali, Payman and Mojahedi, Faezeh and Taghdiri, Maryam and Papari, Elaheh and Soltani Banavandi, Mohammad Javad and Akbari, Saeide and Tonekaboni, Seyed Hassan and Dehghani, Hossein and Ebrahimpour, Mohammad Reza and Bader, Ingrid and Davarnia, Behzad and Cohen, Monika and Khodaei, Hossein and Albrecht, Beate and Azimi, Sarah and Zirn, Birgit and Bastami, Milad and Wieczorek, Dagmar and Bahrami, Gholamreza and Keleman, Krystyna and Vahid, Leila Nouri and Tzschach, Andreas and G{\"a}rtner, Jutta and Gillessen-Kaesbach, Gabriele and Varaghchi, Jamileh Rezazadeh and Timmermann, Bernd and Pourfatemi, Fatemeh and Jankhah, Aria and Chen, Wei and Nikuei, Pooneh and Kalscheuer, Vera M and Oladnabi, Morteza and Wienker, Thomas F and Ropers, Hans-Hilger and Najmabadi, Hossein} } @article {65023, title = {Glia accumulate evidence that actions are futile and suppress unsuccessful behavior.}, journal = {Cell}, volume = {178}, year = {2019}, month = {2019 Jun 27}, pages = {27-43}, abstract = {

When a behavior repeatedly fails to achieve its goal, animals often give up and become passive, which can be strategic for preserving energy or regrouping between attempts. It is unknown how the brain identifies behavioral failures and mediates this behavioral-state switch. In larval zebrafish swimming in virtual reality, visual feedback can be withheld so that swim attempts fail to trigger expected visual flow. After tens of seconds of such motor futility, animals became passive for similar durations. Whole-brain calcium imaging revealed noradrenergic neurons that responded specifically to failed swim attempts and radial astrocytes whose calcium levels accumulated with increasing numbers of failed attempts. Using cell ablation and optogenetic or chemogenetic activation, we found that noradrenergic neurons progressively activated brainstem radial astrocytes, which then suppressed swimming. Thus, radial astrocytes perform a computation critical for behavior: they accumulate evidence that current actions are ineffective and consequently drive changes in behavioral states.

}, doi = {10.1016/j.cell.2019.05.050}, author = {Mu, Yu and Bennett, Davis V and Rubinov, Mikail and Narayan, Sujatha and Yang, Chao-Tsung and Tanimoto, Masashi and Mensh, Brett D and Looger, Loren L and Ahrens, Misha B} } @article {64904, title = {The glutamine transporter Slc38a1 regulates GABAergic neurotransmission and synaptic plasticity.}, journal = {Cerebal Cortex}, year = {2019}, month = {2019 May 03}, abstract = {

GABA signaling sustains fundamental brain functions, from nervous system development to the synchronization of population activity and synaptic plasticity. Despite these pivotal features, molecular determinants underscoring the rapid and cell-autonomous replenishment of the vesicular neurotransmitter GABA and its impact on synaptic plasticity remain elusive. Here, we show that genetic disruption of the glutamine transporter Slc38a1 in mice hampers GABA synthesis, modifies synaptic vesicle morphology in GABAergic presynapses and impairs critical period plasticity. We demonstrate that Slc38a1-mediated glutamine transport regulates vesicular GABA content, induces high-frequency membrane oscillations and shapes cortical processing and plasticity. Taken together, this work shows that Slc38a1 is not merely a transporter accumulating glutamine for metabolic purposes, but a key component regulating several neuronal functions.

}, issn = {1460-2199}, doi = {10.1093/cercor/bhz055}, author = {Qureshi, Tayyaba and S{\o}rensen, Christina and Berghuis, Paul and Jensen, Vidar and Dobszay, Marton B and Farkas, Tam{\'a}s and Dalen, Knut Tomas and Guo, Caiying and Hassel, Bj{\o}rnar and Utheim, Tor Paaske and Hvalby, {\O}ivind and Hafting, Torkel and Harkany, Tibor and Fyhn, Marianne and Chaudhry, Farrukh Abbas} } @article {49509, title = {A GAL80 collection to inhibit GAL4 transgenes in olfactory sensory neurons.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, year = {2018}, month = {2018 Nov 06}, pages = {3661-3668}, abstract = {

Fruit flies recognize hundreds of ecologically relevant odors and respond appropriately to them. The complexity, redundancy and interconnectedness of the olfactory machinery complicate efforts to pinpoint the functional contributions of any component neuron or receptor to behavior. Some contributions can only be elucidated in flies that carry multiple mutations and transgenes, but the production of such flies is currently labor-intensive and time-consuming. Here, we describe a set of transgenic flies that express the GAL80 in specific olfactory sensory neurons (). The GAL80s effectively and specifically subtract the activities of GAL4-driven transgenes that impart anatomical and physiological phenotypes. can allow researchers to efficiently activate only one or a few types of functional neurons in an otherwise nonfunctional olfactory background. Such experiments will improve our understanding of the mechanistic connections between odorant inputs and behavioral outputs at the resolution of only a few functional neurons.

}, issn = {2160-1836}, doi = {10.1534/g3.118.200569}, author = {Eliason, Jessica and Afify, Ali and Potter, Christopher and Matsumura, Lchiro} } @article {49573, title = {Gene flow mediates the role of sex chromosome meiotic drive during complex speciation.}, journal = {eLife}, volume = {7}, year = {2018}, month = {2018 Dec 13}, abstract = {

During speciation, sex chromosomes often accumulate interspecific genetic incompatibilities faster than the rest of the genome. The drive theory posits that sex chromosomes are susceptible to recurrent bouts of meiotic drive and suppression, causing the evolutionary build-up of divergent cryptic sex-linked drive systems and, incidentally, genetic incompatibilities. To assess the role of drive during speciation, we combine high-resolution genetic mapping of X-linked hybrid male sterility with population genomics analyses of divergence and recent gene flow between the fruitfly species, and . Our findings reveal a high density of genetic incompatibilities and a corresponding dearth of gene flow on the X chromosome. Surprisingly, we find that a known drive element recently migrated between species and, rather than contributing to interspecific divergence, caused a strong reduction in local sequence divergence, undermining the evolution of hybrid sterility. Gene flow can therefore mediate the effects of selfish genetic elements during speciation.

}, issn = {2050-084X}, doi = {10.7554/eLife.35468}, author = {Meiklejohn, Colin D and Landeen, Emily L and Gordon, Kathleen E and Rzatkiewicz, Thomas and Kingan, Sarah B and Geneva, Anthony J and Vedanayagam, Jeffrey P and Muirhead, Christina A and Garrigan, Daniel and Stern, David L and Presgraves, Daven C} } @article {49154, title = {Genetic dissection of neural circuits: a decade of progress}, journal = {Neuron}, volume = {98}, year = {2018}, month = {2018 Apr 18}, pages = {256-81}, abstract = {

Tremendous progress has been made since\ Neuron\ published our Primer on genetic dissection of neural circuits 10 years ago. Since then, cell-type-specific anatomical, neurophysiological, and perturbation studies have been carried out in a multitude of invertebrate and vertebrate organisms, linking neurons and circuits to behavioral functions. New methods allow systematic classification of cell types and provide genetic access to diverse neuronal types for studies of connectivity and neural coding during behavior. Here we evaluate key advances over the past decade and discuss future directions.

}, doi = {10.1016/j.neuron.2018.03.040}, author = {Luo, Liqun and Callaway, Edward M and Svoboda, Karel} } @article {49010, title = {A genetically encoded Ca2+ indicator based on circularly permutated sea anemone red fluorescent protein eqFP578.}, journal = {BMC Biology}, volume = {16}, year = {2018}, month = {2018 Jan 16}, pages = {9}, abstract = {

BACKGROUND: Genetically encoded calcium ion (Ca2+) indicators (GECIs) are indispensable tools for measuring Ca2+ dynamics and neuronal activities in vitro and in vivo. Red fluorescent protein (RFP)-based GECIs have inherent advantages relative to green fluorescent protein-based GECIs due to the longer wavelength light used for excitation. Longer wavelength light is associated with decreased phototoxicity and deeper penetration through tissue. Red GECI can also enable multicolor visualization with blue- or cyan-excitable fluorophores.

RESULTS: Here we report the development, structure, and validation of a new RFP-based GECI, K-GECO1, based on a circularly permutated RFP derived from the sea anemone Entacmaea quadricolor. We have characterized the performance of K-GECO1 in cultured HeLa cells, dissociated neurons, stem-cell-derived cardiomyocytes, organotypic brain slices, zebrafish spinal cord in vivo, and mouse brain in vivo.

CONCLUSION: K-GECO1 is the archetype of a new lineage of GECIs based on the RFP eqFP578 scaffold. It offers high sensitivity and fast kinetics, similar or better than those of current state-of-the-art indicators, with diminished lysosomal accumulation and minimal blue-light photoactivation. Further refinements of the K-GECO1 lineage could lead to further improved variants with overall performance that exceeds that of the most highly optimized red GECIs.

}, issn = {1741-7007}, doi = {10.1186/s12915-018-0480-0}, author = {Shen, Yi and Dana, Hod and Abdelfattah, Ahmed S and Patel, Ronak and Shea, Jamien and Molina, Rosana S and Rawal, Bijal and Rancic, Vladimir and Chang, Yu-Fen and Wu, Lanshi and Chen, Yingche and Qian, Yong and Wiens, Matthew D and Hambleton, Nathan and Ballanyi, Klaus and Hughes, Thomas E and Drobizhev, Mikhail and Kim, Douglas S and Koyama, Minoru and Schreiter, Eric R and Campbell, Robert E} } @article {48891, title = {A general method to fine-tune fluorophores for live-cell and in vivo imaging.}, journal = {Nature Methods}, volume = {14}, year = {2017}, month = {2017 Oct}, pages = {987-994}, abstract = {

Pushing the frontier of fluorescence microscopy requires the design of enhanced fluorophores with finely tuned properties. We recently discovered that incorporation of four-membered azetidine rings into classic fluorophore structures elicits substantial increases in brightness and photostability, resulting in the Janelia Fluor (JF) series of dyes. We refined and extended this strategy, finding that incorporation of 3-substituted azetidine groups allows rational tuning of the spectral and chemical properties of rhodamine dyes with unprecedented precision. This strategy allowed us to establish principles for fine-tuning the properties of fluorophores and to develop a palette of new fluorescent and fluorogenic labels with excitation ranging from blue to the far-red. Our results demonstrate the versatility of these new dyes in cells, tissues and animals.

}, keywords = {Animals, Brain, Cell Line, Coloring Agents, Drosophila, Image Processing, Computer-Assisted, Larva, Mice, Microscopy, Fluorescence, Photochemical Processes, Staining and Labeling}, issn = {1548-7105}, doi = {10.1038/nmeth.4403}, author = {Grimm, Jonathan B and Muthusamy, Anand K and Liang, Yajie and Brown, Timothy A and Lemon, William C and Patel, Ronak and Lu, Rongwen and Macklin, John J and Keller, Philipp J and Ji, Na and Lavis, Luke D} } @article {48733, title = {General synthetic method for Si-Fluoresceins and Si-Rhodamines.}, journal = {ACS Central Science}, volume = {3}, year = {2017}, month = {2017 Aug 09}, pages = {975-85}, abstract = {

The century-old fluoresceins and rhodamines persist as flexible scaffolds for fluorescent and fluorogenic compounds. Extensive exploration of these xanthene dyes has yielded general structure{\textendash}activity relationships where the development of new probes is limited only by imagination and organic chemistry. In particular, replacement of the xanthene oxygen with silicon has resulted in new red-shifted Si-fluoresceins and Si-rhodamines, whose high brightness and photostability enable advanced imaging experiments. Nevertheless, efforts to tune the chemical and spectral properties of these dyes have been hindered by difficult synthetic routes. Here, we report a general strategy for the efficient preparation of Si-fluoresceins and Si-rhodamines from readily synthesized bis(2-bromophenyl)silane intermediates. These dibromides undergo metal/bromide exchange to give bis-aryllithium or bis(aryl Grignard) intermediates, which can then add to anhydride or ester electrophiles to afford a variety of Si-xanthenes. This strategy enabled efficient (3{\textendash}5 step) syntheses of known and novel Si-fluoresceins, Si-rhodamines, and related dye structures. In particular, we discovered that previously inaccessible tetrafluorination of the bottom aryl ring of the Si-rhodamines resulted in dyes with improved visible absorbance in solution, and a convenient derivatization through fluoride-thiol substitution. This modular, divergent synthetic method will expand the palette of accessible xanthenoid dyes across the visible spectrum, thereby pushing further the frontiers of biological imaging.

}, doi = {10.1021/acscentsci.7b00247}, author = {Grimm, Jonathan B and Brown, Timothy A and Tkachuk, Ariana N and Lavis, Luke D} } @article {48698, title = {Genetic and neuronal mechanisms governing the sex-specific interaction between sleep and sexual behaviors in Drosophila.}, journal = {Nature Communications}, volume = {8}, year = {2017}, month = {2017 Jul 28}, pages = {154}, abstract = {

Animals execute one particular behavior among many others in a context-dependent manner, yet the mechanisms underlying such behavioral choice remain poorly understood. Here we studied how two fundamental behaviors, sex and sleep, interact at genetic and neuronal levels in Drosophila. We show that an increased need for sleep inhibits male sexual behavior by decreasing the activity of the male-specific P1 neurons that coexpress the sex determination genes fru (M) and dsx, but does not affect female sexual behavior. Further, we delineate a sex-specific neuronal circuit wherein the P1 neurons encoding increased courtship drive suppressed male sleep by forming mutually excitatory connections with the fru (M) -positive sleep-controlling DN1 neurons. In addition, we find that FRU(M) regulates male courtship and sleep through distinct neural substrates. These studies reveal the genetic and neuronal basis underlying the sex-specific interaction between sleep and sexual behaviors in Drosophila, and provide insights into how competing behaviors are co-regulated.Genes and circuits involved in sleep and sexual arousal have been extensively studied in Drosophila. Here the authors identify the sex determination genes fruitless and doublesex, and a sex-specific P1-DN1 neuronal feedback that governs the interaction between these competing behaviors.

}, issn = {2041-1723}, doi = {10.1038/s41467-017-00087-5}, author = {Chen, Dandan and Sitaraman, Divya and Chen, Nan and Jin, Xin and Han, Caihong and Chen, Jie and Sun, Mengshi and Baker, Bruce S and Nitabach, Michael N and Pan, Yufeng} } @article {48319, title = {Genetic and transgenic reagents for Drosophila simulans, D. mauritiana, D. yakuba, D. santomea and D. virilis.}, journal = {G3 (Bethesda, Md.)}, volume = {7}, year = {2017}, month = {2017 Mar 09}, pages = {1339-47}, abstract = {

Species of the Drosophila melanogaster species subgroup, including the species D. simulans, D. mauritiana, D. yakuba, and D. santomea, have long served as model systems for studying evolution. Studies in these species have been limited, however, by a paucity of genetic and transgenic reagents. Here we describe a collection of transgenic and genetic strains generated to facilitate genetic studies within and between these species. We have generated many strains of each species containing mapped piggyBac transposons including an enhanced yellow fluorescent protein gene expressed in the eyes and a phiC31 attP site-specific integration site. We have tested a subset of these lines for integration efficiency and reporter gene expression levels. We have also generated a smaller collection of other lines expressing other genetically encoded fluorescent molecules in the eyes and a number of other transgenic reagents that will be useful for functional studies in these species. In addition, we have mapped the insertion locations of 58 transposable elements in D. virilis that will be useful for genetic mapping studies.

}, issn = {2160-1836}, doi = {10.1534/g3.116.038885}, author = {Stern, David L and Crocker, Justin and Ding, Yun and Frankel, Nicol{\'a}s and Kappes, Gretchen and Kim, Elizabeth and Kuzmickas, Ryan and Lemire, Andrew and Mast, Joshua D and Picard, Serge} } @article {48845, title = {Genetic reagents for making split-GAL4 lines in Drosophila.}, journal = {Genetics }, volume = {209}, year = {2017}, month = {2018 March}, pages = {31-5}, abstract = {

The ability to reproducibly target expression of transgenes to small, defined subsets of cells is a key experimental tool for understanding many biological processes. The Drosophila nervous system contains thousands of distinct cell types and it has generally not been possible to limit expression to one or a few cell types when using a single segment of genomic DNA as an enhancer to drive expression. Intersectional methods, in which expression of the transgene only occurs where two different enhancers overlap in their expression patterns, can be used to achieve the desired specificity. This report describes a set of over 2,800 transgenic lines for use with the split-GAL4 intersectional method.

}, doi = {10.1101/197509}, author = {Dionne, Heather and Hibbard, Karen L and Cavallaro, Amanda and Kao, Jui-Chun and Rubin, Gerald M} } @article {48478, title = {Genetic tools to study juvenile hormone action in Drosophila.}, journal = {Scientific Reports}, volume = {7}, year = {2017}, month = {2017 May 18}, pages = {2132}, abstract = {

The insect juvenile hormone receptor is a basic helix-loop-helix (bHLH), Per-Arnt-Sim (PAS) domain protein, a novel type of hormone receptor. In higher flies like\ Drosophila, the ancestral receptor\ germ cell-expressed\ (gce) gene has duplicated to yield the paralog\ Methoprene-tolerant\ (Met). These paralogous receptors share redundant function during development but play unique roles in adults. Some aspects of JH function apparently require one receptor or the other. To provide a foundation for studying JH receptor function, we have recapitulated endogenous JH receptor expression with single cell resolution. Using Bacteria Artificial Chromosome (BAC) recombineering and a transgenic knock-in, we have generated a spatiotemporal expressional atlas of\ Metand\ gce\ throughout development. We demonstrate JH receptor expression in known JH target tissues, in which temporal expression corresponds with periods of hormone sensitivity. Larval expression largely supports the notion of functional redundancy. Furthermore, we provide the neuroanatomical distribution of JH receptors in both the larval and adult central nervous system, which will serve as a platform for future studies regarding JH action on insect behavior.

}, doi = {10.1038/s41598-017-02264-4}, author = {Baumann, Aaron A and Texada, Michael J and Chen, Hui-Min and Etheredge, Jack N and Miller, D L and Picard, Serge and Warner, Raechel D and Truman, James W and Riddiford, Lynn M} } @article {48732, title = {Genetically encoded biosensors.}, volume = {B2}, number = {14/350,199}, year = {2017}, month = {2017 Aug 01}, edition = {G01N 33/557 (20060101); G01N 33/58 (20060101); C07K 14/435 (20060101); C07K 14/245 (20060101); C07K 14/195 (20060101); G01N 33/68 (20060101)}, abstract = {

The present disclosure provides, inter alia, genetically encoded recombinant peptide biosensors comprising analyte-binding framework portions and signaling portions, wherein the signaling portions are present within the framework portions at sites or amino acid positions that undergo a conformational change upon interaction of the framework portion with an analyte.

}, url = {http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO2\&Sect2=HITOFF\&u=\%2Fnetahtml\%2FPTO\%2Fsearch-adv.htm\&r=2\&p=1\&f=G\&l=50\&d=PTXT\&S1=(\%22Howard+Hughes+medical\%22.ASNM.)\&OS=AN/\%22Howard+Hughes+medical\%22\&RS=AN/\%22Howard+Hughes+medical\%22}, author = {Marvin, Jonathan S and Looger, Loren L and Lee, Richard T and Schreiter, Eric R} } @article {68441, title = {A Genome-Scale Model of Simulates Mechanisms of Metabolic Diversity and Energy Conservation.}, journal = {mSystems}, volume = {2}, year = {2017}, month = {03/2017}, abstract = {

strain WP3 belongs to the group 1 branch of the genus and is a piezotolerant and psychrotolerant species isolated from the deep sea. In this study, a genome-scale model was constructed for WP3 using a combination of genome annotation, ortholog mapping, and physiological verification. The metabolic reconstruction contained 806 genes, 653 metabolites, and 922 reactions, including central metabolic functions that represented nonhomologous replacements between the group 1 and group 2 species. Metabolic simulations with the WP3 model demonstrated consistency with existing knowledge about the physiology of the organism. A comparison of model simulations with experimental measurements verified the predicted growth profiles under increasing concentrations of carbon sources. The WP3 model was applied to study mechanisms of anaerobic respiration through investigating energy conservation, redox balancing, and the generation of proton motive force. Despite being an obligate respiratory organism, WP3 was predicted to use substrate-level phosphorylation as the primary source of energy conservation under anaerobic conditions, a trait previously identified in other species. Further investigation of the ATP synthase activity revealed a positive correlation between the availability of reducing equivalents in the cell and the directionality of the ATP synthase reaction flux. Comparison of the WP3 model with an existing model of a group 2 species, MR-1, revealed that the WP3 model demonstrated greater flexibility in ATP production under the anaerobic conditions. Such flexibility could be advantageous to WP3 for its adaptation to fluctuating availability of organic carbon sources in the deep sea. The well-studied nature of the metabolic diversity of bacteria makes species from this genus a promising platform for investigating the evolution of carbon metabolism and energy conservation. The phylogeny is diverged into two major branches, referred to as group 1 and group 2. While the genotype-phenotype connections of group 2 species have been extensively studied with metabolic modeling, a genome-scale model has been missing for the group 1 species. The metabolic reconstruction of strain WP3 represented the first model for group 1 and the first model among piezotolerant and psychrotolerant deep-sea bacteria. The model brought insights into the mechanisms of energy conservation in WP3 under anaerobic conditions and highlighted its metabolic flexibility in using diverse carbon sources. Overall, the model opens up new opportunities for investigating energy conservation and metabolic adaptation, and it provides a prototype for systems-level modeling of other deep-sea microorganisms.

}, issn = {2379-5077}, doi = {10.1128/mSystems.00165-16}, author = {Dufault-Thompson, Keith and Jian, Huahua and Cheng, Ruixue and Li, Jiefu and Wang, Fengping and Zhang, Ying} } @article {48860, title = {Genomic probes.}, volume = {A1}, number = {US20170268035 }, year = {2017}, month = {2017 Sep 21}, edition = {C12Q 1/68 20060101 C12Q001/68; C12N 15/09 20060101 C12N015/09; C12P 19/34 20060101 C12P019/34; C07H 21/04 20060101 C07H021/04}, abstract = {Labeled probes, and methods of use thereof, comprise a Cas polypeptide conjugated to gRNA that is specific for target nucleic acid sequences, including genomic DNA sequences. The probes and methods can be used to label nucleic acid sequences without global DNA denaturation. The presently-disclosed subject matter meets some or all of the above identified needs, as will become evident to those of ordinary skill in the art after a study of information provided in this document.}, url = {http://appft.uspto.gov/netacgi/nph-Parser?Sect1=PTO1\&Sect2=HITOFF\&d=PG01\&p=1\&u=\%2Fnetahtml\%2FPTO\%2Fsrchnum.html\&r=1\&f=G\&l=50\&s1=\%2220170268035\%22.PGNR.\&OS=DN/20170268035\&RS=DN/20170268035}, author = {Singer, Robert H and Deng, Wulan and Lionnet, Timoth{\'e}e} } @article {48252, title = {The glia of the adult Drosophila nervous system.}, journal = {Glia}, volume = {65}, year = {2017}, month = {2017 Jan 30}, pages = {606-38}, abstract = {

Glia play crucial roles in the development and homeostasis of the nervous system. While the GLIA in the Drosophila embryo have been well characterized, their study in the adult nervous system has been limited. Here, we present a detailed description of the glia in the adult nervous system, based on the analysis of some 500 glial drivers we identified within a collection of synthetic GAL4 lines. We find that glia make up \~{}10\% of the cells in the nervous system and envelop all compartments of neurons (soma, dendrites, axons) as well as the nervous system as a whole. Our morphological analysis suggests a set of simple rules governing the morphogenesis of glia and their interactions with other cells. All glial subtypes minimize contact with their glial neighbors but maximize their contact with neurons and adapt their macromorphology and micromorphology to the neuronal entities they envelop. Finally, glial cells show no obvious spatial organization or registration with neuronal entities. Our detailed description of all glial subtypes and their regional specializations, together with the powerful genetic toolkit we provide, will facilitate the functional analysis of glia in the mature nervous system. GLIA 2017.

}, issn = {1098-1136}, doi = {10.1002/glia.23115}, author = {Kremer, Malte C and Jung, Christophe and Batelli, Sara and Rubin, Gerald M and Gaul, Ulrike} } @article {47524, title = {Genetic and environmental control of neurodevelopmental robustness in Drosophila.}, journal = {PLoS One}, volume = {11}, year = {2016}, month = {2016 May 25}, pages = {e0155957}, abstract = {

Interindividual differences in neuronal wiring may contribute to behavioral individuality and affect susceptibility to neurological disorders. To investigate the causes and potential consequences of wiring variation in Drosophila melanogaster, we focused on a hemilineage of ventral nerve cord interneurons that exhibits morphological variability. We find that late-born subclasses of the 12A hemilineage are highly sensitive to genetic and environmental variation. Neurons in the second thoracic segment are particularly variable with regard to two developmental decisions, whereas its segmental homologs are more robust. This variability "hotspot" depends on Ultrabithorax expression in the 12A neurons, indicating variability is cell-intrinsic and under genetic control. 12A development is more variable and sensitive to temperature in long-established laboratory strains than in strains recently derived from the wild. Strains with a high frequency of one of the 12A variants also showed a high frequency of animals with delayed spontaneous flight initiation, whereas other wing-related behaviors did not show such a correlation and were thus not overtly affected by 12A variation. These results show that neurodevelopmental robustness is variable and under genetic control in Drosophila and suggest that the fly may serve as a model for identifying conserved gene pathways that stabilize wiring in stressful developmental environments. Moreover, some neuronal lineages are variation hotspots and thus may be more amenable to evolutionary change.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0155957}, author = {Mellert, David J and Williamson, W Ryan and Shirangi, Troy R and Card, Gwyneth M and Truman, James W} } @article {47726, title = {The genome of the crustacean Parhyale hawaiensis: a model for animal development, regeneration, immunity and lignocellulose digestion.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Nov 16}, pages = {e20062}, abstract = {

Parhyale hawaiensis is a blossoming model system for studies of developmental mechanisms and more recently adult regeneration. We have sequenced the genome allowing annotation of all key signaling pathways, small non-coding RNAs and transcription factors that will enhance ongoing functional studies. Parhayle is a member of the Malacostraca, which includes crustacean food crop species. We analysed the immunity related genes of Parhyale as an important comparative system for these species, where immunity related aquaculture problems have increased as farming has intensified. We also find that Parhyale and other species within Multicrustacea contain the enzyme sets necessary to perform lignocellulose digestion (wood eating), suggesting this ability may predate the diversification of this lineage. Our data provide an essential resource for further development of the Parhyale model. The first Malacostracan genome sequence will underpin ongoing comparative work in important food crop species and research investigating lignocellulose as energy source.

Publication first appeared in BioRxiv on August 2, 2016.\ http://dx.doi.org/10.1101/065789

}, doi = {10.7554/eLife.20062}, author = {Kao, Damian and Lai, Alvina G and Stamataki, Evangelia and Rosic, Silvana and Konstantinides, Nikolaos and Jarvis, Erin and Di Donfrancesco, Alessia and Pouchkina-Stantcheva, Natalia and Semon, Marie and Grillo, Marco and Bruce, Heather and Kumar, Suyash and Siwanowicz, Igor and Le, Andy and Lemire, Andrew and Extavour, Cassandra and Browne, William and Wolff, Carsten and Averof, Michalis and et al} } @article {47547, title = {GFP-aequorin protein sensor for ex~vivo and in~vivo imaging of Ca(2+) dynamics in high-Ca(2+) organelles.}, journal = {Cell Chemical Biology}, year = {2016}, month = {2016 Jun 1}, abstract = {

Proper functioning of organelles such as the ER or the Golgi apparatus requires luminal accumulation of Ca(2+) at high concentrations. Here we describe a\ ratiometric low-affinity Ca(2+) sensor of the GFP-aequorin protein (GAP) family optimized for measurements in high-Ca(2+) concentration environments. Transgenic animals expressing the ER-targeted sensor allowed monitoring of Ca(2+) signals inside the organelle. The use of the sensor was demonstrated under three experimental paradigms: (1) ER Ca(2+) oscillations in cultured astrocytes, (2) ex\ vivo functional mapping of cholinergic receptors triggering ER Ca(2+) release in acute hippocampal slices from transgenic mice, and (3) in\ vivo sarcoplasmic reticulum Ca(2+) dynamics in the muscle of transgenic flies. Our results provide proof of the suitability of the new biosensors to monitor Ca(2+) dynamics inside intracellular organelles under physiological conditions and open an avenue to explore complex Ca(2+) signaling in animal models of health and disease.

}, issn = {2451-9456}, doi = {10.1016/j.chembiol.2016.05.010}, author = {Navas-Navarro, Paloma and Rojo-Ruiz, Jonathan and Rodriguez-Prados, Macarena and Ganfornina, Mar{\'\i}a Dolores and Looger, Loren L and Alonso, Mar{\'\i}a Teresa and Garc{\'\i}a-Sancho, Javier} } @article {48094, title = {Global collaboration, learning from other fields.}, journal = {Neuron}, volume = {92}, year = {2016}, month = {2016 Nov 2}, pages = {561-563}, abstract = {

Neuroscience research is becoming increasingly more collaborative and interdisciplinary with partnerships between industry and academia and insights from fields beyond neuroscience. In the age of institutional initiatives and multi-investigator collaborations, scientists from around the world shared their perspectives on the effectiveness of large-scale collaborations versus single-lab, hypothesis-driven science.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2016.10.040} } @article {47967, title = {Glutamate-induced RNA localization and translation in neurons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, year = {2016}, month = {2016 Sep 13}, abstract = {

Localization of mRNA is required for protein synthesis to occur within discrete intracellular compartments. Neurons represent an ideal system for studying the precision of mRNA trafficking because of their polarized structure and the need for synapse-specific targeting. To investigate this targeting, we derived a quantitative and analytical approach. Dendritic spines were stimulated by glutamate uncaging at a diffraction-limited spot, and the localization of single β-actin mRNAs was measured in space and time. Localization required NMDA receptor activity, a dynamic actin cytoskeleton, and the transacting RNA-binding protein, Zipcode-binding protein 1 (ZBP1). The ability of the mRNA to direct newly synthesized proteins to the site of localization was evaluated using a Halo-actin reporter so that RNA and protein were detected simultaneously. Newly synthesized Halo-actin was enriched at the site of stimulation, required NMDA receptor activity, and localized preferentially at the periphery of spines. This work demonstrates that synaptic activity can induce mRNA localization and local translation of β-actin where the new actin participates in stabilizing the expanding synapse in dendritic spines.

}, doi = {10.1073/pnas.1614267113}, author = {Yoon, Young J and Wu, Bin and Buxbaum, Adina R and Das, Sulagna and Tsai, Albert and English, Brian P and Grimm, Jonathan B and Lavis, Luke D and Singer, Robert H} } @article {46267, title = {A general method to improve fluorophores for live-cell and single-molecule microscopy.}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015 Jan 19}, pages = {244-50}, abstract = {

Specific labeling of biomolecules with bright fluorophores is the keystone of fluorescence microscopy. Genetically encoded self-labeling tag proteins can be coupled to synthetic dyes inside living cells, resulting in brighter reporters than fluorescent proteins. Intracellular labeling using these techniques requires cell-permeable fluorescent ligands, however, limiting utility to a small number of classic fluorophores. Here we describe a simple structural modification that improves the brightness and photostability of dyes while preserving spectral properties and cell permeability. Inspired by molecular modeling, we replaced the N,N-dimethylamino substituents in tetramethylrhodamine with four-membered azetidine rings. This addition of two carbon atoms doubles the quantum efficiency and improves the photon yield of the dye in applications ranging from in vitro single-molecule measurements to super-resolution imaging. The novel substitution is generalizable, yielding a palette of chemical dyes with improved quantum efficiencies that spans the UV and visible range.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3256}, author = {Grimm, Jonathan B and English, Brian P and Chen, Jiji and Slaughter, Joel P and Zhang, Zhengjian and Revyakin, Andrey and Patel, Ronak and Macklin, John J and Normanno, Davide and Singer, Robert H and Lionnet, Timoth{\'e}e and Lavis, Luke D} } @article {46549, title = {Generating customized transgene landing sites and multi-transgene arrays in Drosophila using phiC31 integrase.}, journal = {Genetics}, volume = {199}, year = {2015}, month = {2015 Apr}, pages = {919-34}, abstract = {

Transgenesis in numerous eukaryotes has been facilitated by the use of site-specific integrases to stably insert transgenes at predefined genomic positions (landing sites). However, the utility of integrase-mediated transgenesis in any system is constrained by the limited number and variable expression properties of available landing sites. By exploiting the nonstandard recombination activity exhibited by a phiC31 integrase mutant, we developed a rapid and inexpensive method for isolating landing sites that exhibit desired expression properties. Additionally, we devised a simple technique for constructing arrays of transgenes at a single landing site, thereby extending the utility of previously characterized landing sites. Using the fruit fly Drosophila melanogaster, we demonstrate the feasibility of these approaches by isolating new landing sites optimized to express transgenes in the nervous system and by building fluorescent reporter arrays at several landing sites. Because these strategies require the activity of only a single exogenous protein, we anticipate that they will be portable to species such as nonmodel organisms, in which genetic manipulation is more challenging, expediting the development of genetic resources in these systems.

}, issn = {1943-2631}, doi = {10.1534/genetics.114.173187}, author = {Knapp, Jon-Michael and Chung, Phuong and Simpson, Julie H} } @article {46535, title = {Genetic architecture and functional characterization of genes underlying the rapid diversification of male external genitalia between Drosophila simulans and Drosophila mauritiana.}, journal = {Genetics}, year = {2015}, month = {2015 Mar 16}, abstract = {

Male sexual characters are often among the first traits to diverge between closely related species and identifying the genetic basis of such changes can contribute to our understanding of their evolutionary history. However, little is known about the genetic architecture or the specific genes underlying the evolution of male genitalia. The morphology of the claspers, posterior lobes and anal plates exhibit striking differences between Drosophila mauritiana and Drosophila simulans. Using QTL and introgression-based high-resolution mapping, we identified several small regions on chromosome arms 3L and 3R that contribute to differences in these traits. However, we found that the loci underlying the evolution of clasper differences between these two species are independent from those that contribute to posterior lobe and anal plate divergence. Furthermore, while most of the loci affect each trait in the same direction and act additively, we also found evidence for epistasis between loci for clasper bristle number. In addition, we conducted an RNAi screen in D. melanogaster to investigate if positional and expression candidate genes located on chromosome 3L, are also involved in genital development. We found that six of these genes, including components of Wnt signaling and male-specific lethal 3 (msl3), regulate the development of genital traits consistent with the effects of the introgressed regions where they are located and that thus represent promising candidate genes for the evolution these traits.

}, issn = {1943-2631}, doi = {10.1534/genetics.114.174045}, author = {Tanaka, Kentaro M and Hopfen, Corinna and Herbert, Matthew R and Schl{\"o}tterer, Christian and Stern, David L and Masly, John P and McGregor, Alistair P and Nunes, Maria D S} } @article {47896, title = {Genome engineering of isogenic human ES cells to model autism disorders.}, journal = {Nucleic acids research}, volume = {43}, year = {2015}, month = {2015 May 26}, pages = {e65}, abstract = {

Isogenic pluripotent stem cells are critical tools for studying human neurological diseases by allowing one to study the effects of a mutation in a fixed genetic background. Of particular interest are the spectrum of autism disorders, some of which are monogenic such as Timothy syndrome (TS); others are multigenic such as the microdeletion and microduplication syndromes of the 16p11.2 chromosomal locus. Here, we report engineered human embryonic stem cell (hESC) lines for modeling these two disorders using locus-specific endonucleases to increase the efficiency of homology-directed repair (HDR). We developed a system to: (1) computationally identify unique transcription activator-like effector nuclease (TALEN) binding sites in the genome using a new software program, TALENSeek, (2) assemble the TALEN genes by combining golden gate cloning with modified constructs from the FLASH protocol, and (3) test the TALEN pairs in an amplification-based HDR assay that is more sensitive than the typical non-homologous end joining assay. We applied these methods to identify, construct, and test TALENs that were used with HDR donors in hESCs to generate an isogenic TS cell line in a scarless manner and to model the 16p11.2 copy number disorder without modifying genomic loci with high sequence similarity.

}, keywords = {Autistic Disorder, Binding Sites, Cell Engineering, Cell Line, Child Development Disorders, Pervasive, Deoxyribonucleases, Embryonic Stem Cells, Gene Targeting, Genome, Human, Humans, Long QT Syndrome, Models, Genetic, Recombinational DNA Repair, Software, Syndactyly}, issn = {1362-4962}, doi = {10.1093/nar/gkv164}, author = {Martinez, Refugio A and Stein, Jason L and Krostag, Anne-Rachel F and Nelson, Angelique M and Marken, John S and Menon, Vilas and May, Ryan C and Yao, Zizhen and Kaykas, Ajamete and Geschwind, Daniel H and Grimley, Joshua S} } @article {47014, title = {Genome-wide errant targeting by Hairy.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Aug 25}, abstract = {

Metazoan transcriptional repressors regulate chromatin through diverse histone modifications. Contributions of individual factors to the chromatin landscape in development is difficult to establish, as global surveys reflect multiple changes in regulators. Therefore, we studied the conserved Hairy/Enhancer of Split family repressor Hairy, analyzing histone marks and gene expression in Drosophila embryos. This long-range repressor mediates histone acetylation and methylation in large blocks, with highly context-specific effects on target genes. Most strikingly, Hairy exhibits biochemical activity on many loci that are uncoupled to changes in gene expression. Rather than representing inert binding sites, as suggested for many eukaryotic factors, many regions are targeted errantly by Hairy to modify the chromatin landscape. Our findings emphasize that identification of active cis-regulatory elements must extend beyond the survey of prototypical chromatin marks. We speculate that this errant activity may provide a path for creation of new regulatory elements, facilitating the evolution of novel transcriptional circuits.

}, issn = {2050-084X}, doi = {10.7554/eLife.06394}, author = {Kok, Kurtulus and Ay, Ahmet and Li, Li M and Arnosti, David N} } @article {46756, title = {Genomic signatures of evolutionary transitions from solitary to group living.}, journal = {Science}, year = {2015}, month = {2015 May 14}, abstract = {

The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of ten bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks.

}, issn = {1095-9203}, doi = {10.1126/science.aaa4788}, author = {Kapheim, Karen M and Pan, Hailin and Li, Cai and Salzberg, Steven L and Puiu, Daniela and Magoc, Tanja and Robertson, Hugh M and Hudson, Matthew E and Venkat, Aarti and Fischman, Brielle J and Hernandez, Alvaro and Yandell, Mark and Ence, Daniel and Holt, Carson and Yocum, George D and Kemp, William P and Bosch, Jordi and Waterhouse, Robert M and Zdobnov, Evgeny M and Stolle, Eckart and Kraus, F Bernhard and Helbing, Sophie and Moritz, Robin F A and Glastad, Karl M and Hunt, Brendan G and Goodisman, Michael A D and Hauser, Frank and Grimmelikhuijzen, Cornelis J P and Pinheiro, Daniel Guariz and Nunes, Francis Morais Franco and Soares, Michelle Prioli Miranda and Tanaka, {\'E}rica Donato and Sim{\~o}es, Zil{\'a} Luz Paulino and Hartfelder, Klaus and Evans, Jay D and Barribeau, Seth M and Johnson, Reed M and Massey, Jonathan H and Southey, Bruce R and Hasselmann, Martin and Hamacher, Daniel and Biewer, Matthias and Kent, Clement F and Zayed, Amro and Blatti, Charles and Sinha, Saurabh and Johnston, J Spencer and Hanrahan, Shawn J and Kocher, Sarah D and Wang, Jun and Robinson, Gene E and Zhang, Guojie} } @article {47084, title = {Green-to-red photoconversion of GCaMP.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015 Sep 18}, pages = {e0138127}, abstract = {

Genetically encoded calcium indicators (GECIs) permit imaging intracellular calcium transients. Among GECIs, the GFP-based GCaMPs are the most widely used because of their high sensitivity and rapid response to changes in intracellular calcium concentrations. Here we report that the fluorescence of GCaMPs-including GCaMP3, GCaMP5 and GCaMP6-can be converted from green to red following exposure to blue-green light (450-500 nm). This photoconversion occurs in both insect and mammalian cells and is enhanced in a low oxygen environment. The red fluorescent GCaMPs retained calcium responsiveness, albeit with reduced sensitivity. We identified several amino acid residues in GCaMP important for photoconversion and generated a GCaMP variant with increased photoconversion efficiency in cell culture. This light-induced spectral shift allows the ready labeling of specific, targeted sets of GCaMP-expressing cells for functional imaging in the red channel. Together, these findings indicate the potential for greater utility of existing GCaMP reagents, including transgenic animals.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0138127}, author = {Ai, Minrong and Mills, Holly and Kanai, Makoto and Lai, Jason and Deng, Jingjing and Schreiter, Eric and Looger, Loren and Neubert, Thomas and Suh, Greg} } @article {45334, title = {A GAL4 driver resource for developmental and behavioral studies on the larval CNS of Drosophila.}, journal = {Cell Reports}, volume = {8}, year = {2014}, month = {2014 Aug 7}, pages = {897-908}, abstract = {

We report the larval CNS expression patterns for 6,650 GAL4 lines based on cis-regulatory regions (CRMs) from the Drosophila genome. Adult CNS expression patterns were previously reported for this collection, thereby providing a unique resource for determining the origins of adult cells. An illustrative example reveals the origin of the astrocyte-like glia of the ventral\ CNS. Besides larval neurons and glia, the larval CNS\ contains scattered lineages of immature, adult-specific\ neurons. Comparison of lineage expression within this large collection of CRMs provides insight into the codes used for designating neuronal types. The CRMs encode both dense and sparse patterns of lineage expression. There is little correlation between brain and thoracic lineages in patterns of sparse expression, but expression in the two regions is highly correlated in the dense mode. The optic lobes, by comparison, appear to use a different set of genetic instructions in their development.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2014.06.065}, author = {Li, Hsing-Hsi and Kroll, Jason R and Lennox, Sara M and Ogundeyi, Omotara and Jeter, Jennifer and Depasquale, Gina and Truman, James W} } @article {46703, title = {Gene regulation: the HSP70 gene jumps when shocked.}, journal = {Current Biology}, volume = {24}, year = {2014}, month = {2014 May 19}, pages = {R396-8}, abstract = {

Limited chromosome mobility has been observed in mammalian interphase nuclei. Live imaging shows unidirectional and actin-dependent movement of HSP70 loci towards speckles upon heat shock, resulting in enhanced transcription. This adds further impetus to understanding compartmentalization of function in the nucleus.

}, keywords = {Animals, Heat-Shock Response, Humans, Transcriptional Activation, Transgenes}, issn = {1879-0445}, doi = {10.1016/j.cub.2014.03.070}, author = {Vera, Maria and Singer, Robert H} } @article {6882, title = {Generating mosaics for lineage analysis in flies.}, journal = {Wiley Interdisciplinary Reviews - Developmental Biology}, volume = {3}, year = {2014}, month = {2014 Jan}, pages = {69-81}, abstract = {

By generating and studying mosaic organisms, we are learning how intricate tissues form as cells proliferate and diversify through organism development. FLP/FRT-mediated site-specific mitotic recombination permits the generation of mosaic flies with efficiency and control. With heat-inducible or tissue-specific FLP transgenes at our disposal, we can engineer mosaics carrying clones of homozygous cells that come from specific pools of heterozygous precursors. This permits detailed cell lineage analysis followed by mosaic analysis of gene functions in the underlying developmental processes. Expression of transgenes (e.g., reporters) only in the homozygous cells enables mosaic analysis in the complex nervous system. Tracing neuronal lineages by using mosaics revolutionized mechanistic studies of neuronal diversification and differentiation, exemplifying the power of genetic mosaics in developmental biology. WIREs Dev Biol 2014, 3:69{\textendash}81. doi: 10.1002/wdev.122

}, issn = {1759-7684}, doi = {10.1002/wdev.122}, author = {Lee, Tzumin} } @article {6709, title = {Genetic identification and separation of innate and experience-dependent courtship behaviors in Drosophila.}, journal = {Cell}, volume = {156}, year = {2014}, month = {2014 Jan 16}, pages = {236-48}, abstract = {

Wild-type D.\ melanogaster males innately possess the ability to perform a multistep courtship ritual to conspecific females. The potential for this behavior is specified by the male-specific products of the fruitless (fru(M)) gene; males without fru(M) do not court females when held in isolation. We show that such fru(M) null males acquire the potential for courtship when grouped with other flies; they apparently learn to court flies with which they were grouped, irrespective of sex or species and retain this behavior for at least a week. The male-specific product of the doublesex gene (dsx(M)) is necessary and sufficient for the acquisition of the potential for such experience-dependent courtship. These results reveal a process that builds, via dsx(M) and social experience, the potential for a more flexible sexual behavior, which could be evolutionarily conserved as dsx-related genes that function in sexual development are found throughout the animal kingdom.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2013.11.041}, author = {Pan, Yufeng and Baker, Bruce S} } @article {45696, title = {A genetically specified connectomics approach applied to long-range feeding regulatory circuits.}, journal = {Nature Neuroscience}, volume = {17}, year = {2014}, month = {2014 Dec}, pages = {1830-9}, abstract = {

Synaptic connectivity and molecular composition provide a blueprint for information processing in neural circuits. Detailed structural analysis of neural circuits requires nanometer resolution, which can be obtained with serial-section electron microscopy. However, this technique remains challenging for reconstructing molecularly defined synapses. We used a genetically encoded synaptic marker for electron microscopy (GESEM) based on intra-vesicular generation of electron-dense labeling in axonal boutons. This approach allowed the identification of synapses from Cre recombinase-expressing or GAL4-expressing neurons in the mouse and fly with excellent preservation of ultrastructure. We applied this tool to visualize long-range connectivity of AGRP and POMC neurons in the mouse, two molecularly defined hypothalamic populations that are important for feeding behavior. Combining selective ultrastructural reconstruction of neuropil with functional and viral circuit mapping, we characterized some basic features of circuit organization for axon projections of these cell types. Our findings demonstrate that GESEM labeling enables long-range connectomics with molecularly defined cell types.

}, issn = {1546-1726}, doi = {10.1038/nn.3854}, author = {Atasoy, Deniz and Betley, J Nicholas and Li, Wei-Ping and Su, Helen H and Sertel, Sinem M and Scheffer, Louis K and Simpson, Julie H and Fetter, Richard D and Sternson, Scott M} } @article {45099, title = {Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis.}, journal = {Science}, volume = {344}, year = {2014}, month = {2014 Apr 25}, pages = {380-6}, abstract = {

Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein-encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology.

}, keywords = {Animals, Blood, Feeding Behavior, Female, Genes, Insect, Genome, Insect, Insect Proteins, Insect Vectors, Microbiota, Molecular Sequence Annotation, Molecular Sequence Data, Reproduction, Salivary Glands, Sensation, Sequence Analysis, DNA, Symbiosis, Trypanosoma, Trypanosomiasis, African, Tsetse Flies, Wolbachia}, issn = {1095-9203}, doi = {10.1126/science.1249656} } @article {6954, title = {Genome-wide identification of Drosophila Hb9 targets reveals a pivotal role in directing the transcriptome within eight neuronal lineages, including activation of nitric oxide synthase and Fd59a/Fox-D.}, journal = {Developmental Biology}, volume = {388}, year = {2014}, month = {2014 Apr 1}, pages = {117-33}, abstract = {

Hb9 is a homeodomain-containing transcription factor that acts in combination with Nkx6, Lim3, and Tail-up (Islet) to guide the stereotyped differentiation, connectivity, and function of a subset of neurons in Drosophila. The role of Hb9 in directing neuronal differentiation is well documented, but the lineage of Hb9(+) neurons is only partly characterized, its regulation is poorly understood, and most of the downstream genes through which it acts remain at large. Here, we complete the lineage tracing of all embryonic Hb9(+) neurons (to eight neuronal lineages) and provide evidence that hb9, lim3, and tail-up are coordinately regulated by a common set of upstream factors. Through the parallel use of micro-array gene expression profiling and the Dam-ID method, we searched for Hb9-regulated genes, uncovering transcription factors as the most over-represented class of genes regulated by Hb9 (and Nkx6) in the CNS. By a nearly ten-to-one ratio, Hb9 represses rather than activates transcription factors, highlighting transcriptional repression of other transcription factors as a core mechanism by which Hb9 governs neuronal determination. From the small set of genes activated by Hb9, we characterized the expression and function of two - fd59a/foxd, which encodes a transcription factor, and Nitric oxide synthase. Under standard lab conditions, both genes are dispensable for Drosophila development, but Nos appears to inhibit hyper-active behavior and fd59a appears to act in octopaminergic neurons to control egg-laying behavior. Together our data clarify the mechanisms through which Hb9 governs neuronal specification and differentiation and provide an initial characterization of the expression and function of Nos and fd59a in the Drosophila CNS.

}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2014.01.029}, author = {Lacin, Haluk and Rusch, Jannette and Yeh, Raymond T and Fujioka, Miki and Wilson, Beth A and Zhu, Yi and Robie, Alice A and Mistry, Hemlata and Wang, Ting and Jaynes, James B and Skeath, James B} } @article {45592, title = {A giant fibre bypass for the fly.}, journal = {Journal of Experimental Biology}, volume = {217}, year = {2014}, month = {2014 Oct 24}, pages = {2988-89}, doi = {10.1242/​jeb.095000 }, author = {Zwart, Maarten} } @article {6934, title = {Graph-based active learning of agglomeration (GALA): a Python library to segment 2D and 3D neuroimages}, journal = {Frontiers in Neuroinformatics}, volume = {8}, year = {2014}, month = {2014 Apr 4}, pages = {34}, abstract = {

The aim in high-resolution connectomics is to reconstruct complete neuronal connectivity in a tissue. Currently, the only technology capable of resolving the smallest neuronal processes is electron microscopy (EM). Thus, a common approach to network reconstruction is to perform (error-prone) automatic segmentation of EM images, followed by manual proofreading by experts to fix errors. We have developed an algorithm and software library to not only improve the accuracy of the initial automatic segmentation, but also point out the image coordinates where it is likely to have made errors. Our software, called gala (graph-based active learning of agglomeration), improves the state of the art in agglomerative image segmentation. It is implemented in Python and makes extensive use of the scientific Python stack (numpy, scipy, networkx, scikit-learn, scikit-image, and others). We present here the software architecture of the gala library, and discuss several designs that we consider would be generally useful for other segmentation packages. We also discuss the current limitations of the gala library and how we intend to address them.

}, issn = {1662-5196}, doi = {10.3389/fninf.2014.00034}, author = {Nunez-Iglesias, Juan and Kennedy, Ryan and Plaza, Stephen M and Chakraborty, Anirban and William T. Katz} } @article {6923, title = {Genetic and neural mechanisms that inhibit Drosophila from mating with other species.}, journal = {Cell}, volume = {154}, year = {2013}, month = {2013 Jul 3}, pages = {89-102}, abstract = {

Genetically hard-wired neural mechanisms must enforce behavioral reproductive isolation because interspecies courtship is rare even in sexually na{\"{\i}ve animals of most species. We find that the chemoreceptor Gr32a inhibits male D. melanogaster from courting diverse fruit fly species. Gr32a recognizes nonvolatile aversive cues present on these reproductively dead-end targets, and activity of Gr32a neurons is necessary and sufficient to inhibit interspecies courtship. Male-specific Fruitless (Fru(M)), a master regulator of courtship, also inhibits interspecies courtship. Gr32a and Fru(M) are not coexpressed, but Fru(M) neurons contact Gr32a neurons, suggesting that these genes influence a shared neural circuit that inhibits interspecies courtship. Gr32a and Fru(M) also suppress within-species intermale courtship, but we show that distinct mechanisms preclude sexual displays toward conspecific males and other species. Although this chemosensory pathway does not inhibit interspecies mating in D. melanogaster females, similar mechanisms appear to inhibit this behavior in many other male drosophilids.

}, keywords = {Animal, Animals, Cell Surface, Courtship, Drosophila, Drosophila melanogaster, Drosophila Proteins, Female, Genetic Speciation, Male, Mating Preference, Nerve Tissue Proteins, Neurons, Receptors, Transcription Factors}, issn = {1097-4172}, doi = {10.1016/j.cell.2013.06.008}, author = {Fan, Pu and Manoli, Devanand S and Ahmed, Osama M and Chen, Yi and Agarwal, Neha and Kwong, Sara and Cai, Allen G and Neitz, Jeffrey and Renslo, Adam and Baker, Bruce S and Shah, Nirao M} } @article {6477, title = {The genetic causes of convergent evolution.}, journal = {Nature Reviews Genetics}, volume = {14}, year = {2013}, month = {2013 Oct 9}, pages = {751-4}, type = {Review}, abstract = {

The evolution of phenotypic similarities between species, known as convergence, illustrates that populations can respond predictably to ecological challenges. Convergence often results from similar genetic changes, which can emerge in two ways: the evolution of similar or identical mutations in independent lineages, which is termed parallel evolution; and the evolution in independent lineages of alleles that are shared among populations, which I call collateral genetic evolution. Evidence for parallel and collateral evolution has been found in many taxa, and an emerging hypothesis is that they result from the fact that mutations in some genetic targets minimize pleiotropic effects while simultaneously maximizing adaptation. If this proves correct, then the molecular changes underlying adaptation might be more predictable than has been appreciated previously.

}, issn = {1471-0064}, doi = {10.1038/nrg3483advance online publication}, author = {Stern, David L} } @article {6126, title = {Genetically encoded calcium indicators and astrocyte calcium microdomains.}, journal = {The Neuroscientist : A Review Journal Bringing Neurobiology, Neurology and Psychiatry}, volume = {19}, year = {2013}, month = {2013 Jun}, pages = {274-91}, abstract = {

The discovery of intracellular Ca(2+) signals within astrocytes has changed our view of how these ubiquitous cells contribute to brain function. Classically thought merely to serve supportive functions, astrocytes are increasingly thought to respond to, and regulate, neurons. The use of organic Ca(2+) indicator dyes such as Fluo-4 and Fura-2 has proved instrumental in the study of astrocyte physiology. However, progress has recently been accelerated by the use of cytosolic and membrane targeted genetically encoded calcium indicators (GECIs). Herein, we review these recent findings, discuss why studying astrocyte Ca(2+) signals is important to understand brain function, and summarize work that led to the discovery of TRPA1 channel-mediated near-membrane Ca(2+) signals in astrocytes and their indirect neuromodulatory roles at inhibitory synapses in the CA1 stratum radiatum region of the hippocampus. We suggest that the use of membrane-targeted and cytosolic GECIs holds great promise to explore the diversity of Ca(2+) signals within single astrocytes and also to study diversity of function for astrocytes in different parts of the brain.

}, issn = {1089-4098}, doi = {10.1177/1073858412468794}, author = {Tong, Xiaoping and Shigetomi, Eiji and Looger, Loren L and Khakh, Baljit S.} } @article {6541, title = {Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics.}, journal = {Frontiers in Molecular Neuroscience}, volume = {6}, year = {2013}, month = {2013 Mar 4}, pages = {2}, abstract = {

Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Here we describe red, single-wavelength GECIs, "RCaMPs," engineered from circular permutation of the thermostable red fluorescent protein mRuby. High-resolution crystal structures of mRuby, the red sensor RCaMP, and the recently published red GECI R-GECO1 give insight into the chromophore environments of the Ca(2+)-bound state of the sensors and the engineered protein domain interfaces of the different indicators. We characterized the biophysical properties and performance of RCaMP sensors in vitro and in vivo in Caenorhabditis elegans, Drosophila larvae, and larval zebrafish. Further, we demonstrate 2-color calcium imaging both within the same cell (registering mitochondrial and somatic [Ca(2+)]) and between two populations of cells: neurons and astrocytes. Finally, we perform integrated optogenetics experiments, wherein neural activation via channelrhodopsin-2 (ChR2) or a red-shifted variant, and activity imaging via RCaMP or GCaMP, are conducted simultaneously, with the ChR2/RCaMP pair providing independently addressable spectral channels. Using this paradigm, we measure calcium responses of naturalistic and ChR2-evoked muscle contractions in vivo in crawling C. elegans. We systematically compare the RCaMP sensors to R-GECO1, in terms of action potential-evoked fluorescence increases in neurons, photobleaching, and photoswitching. R-GECO1 displays higher Ca(2+) affinity and larger dynamic range than RCaMP, but exhibits significant photoactivation with blue and green light, suggesting that integrated channelrhodopsin-based optogenetics using R-GECO1 may be subject to artifact. Finally, we create and test blue, cyan, and yellow variants engineered from GCaMP by rational design. This engineered set of chromatic variants facilitates new experiments in functional imaging and optogenetics.

}, issn = {1662-5099}, doi = {10.3389/fnmol.2013.00002}, author = {Akerboom, Jasper and Carreras Calder{\'o}n, Nicole and Tian, Lin and Wabnig, Sebastian and Prigge, Matthias and Tol{\"o}, Johan and Gordus, Andrew and Orger, Michael B. and Severi, Kristen E and Macklin, John J and Patel, Ronak and Pulver, Stefan R and Wardill, Trevor J. and Fischer, Elisabeth and Sch{\"u}ler, Christina and Chen, Tsai-Wen and Sarkisyan, Karen S and Marvin, Jonathan S and Bargmann, Cornelia I and Kim, Douglas S. and K{\"u}gler, Sebastian and Lagnado, Leon and Hegemann, Peter and Gottschalk, Alexander and Schreiter, Eric R and Looger, Loren L} } @article {5423, title = {A GAL4-driver line resource for Drosophila neurobiology.}, journal = {Cell Reports}, volume = {2}, year = {2012}, month = {2012 Oct 25}, pages = {991-1001}, abstract = {

We established a collection of 7,000 transgenic lines of Drosophila melanogaster. Expression of GAL4 in each line is controlled by a different, defined fragment of genomic DNA that serves as a transcriptional enhancer. We used confocal microscopy of dissected nervous systems to determine the expression patterns driven by each fragment in the adult brain and ventral nerve cord. We present image data on 6,650 lines. Using both manual and machine-assisted annotation, we describe the expression patterns in the most useful lines. We illustrate the utility of these data for identifying novel neuronal cell types, revealing brain asymmetry, and describing the nature and extent of neuronal shape stereotypy. The GAL4 lines allow expression of exogenous genes in distinct, small subsets of the adult nervous system. The set of DNA fragments, each driving a documented expression pattern, will facilitate the generation of additional constructs for manipulating neuronal function. synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

For the overall strategy and methods used to produce the GAL4 lines:
Pfeiffer, B.D., Jenett, A., Hammonds, A.S., Ngo, T.T., Misra, S., Murphy, C., Scully, A., Carlson, J.W., Wan, K.H., Laverty, T.R., Mungall, C., Svirskas, R., Kadonaga, J.T., Doe, C.Q., Eisen, M.B., Celniker, S.E., Rubin, G.M. (2008). Tools for neuroanatomy and neurogenetics in Drosophila. Proc. Natl. Acad. Sci. USA 105, 9715-9720. http://www.pnas.org/content/105/28/9715.full.pdf+html synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

For data on expression in the embryo:
Manning, L., Purice, M.D., Roberts, J., Pollard, J.L., Bennett, A.L., Kroll, J.R., Dyukareva, A.V., Doan, P.N., Lupton, J.R., Strader, M.E., Tanner, S., Bauer, D., Wilbur, A., Tran, K.D., Laverty, T.R., Pearson, J.C., Crews, S.T., Rubin, G.M., and Doe, C.Q. (2012) Annotated embryonic CNS expression patterns of 5000 GMR GAL4 lines: a resource for manipulating gene expression and analyzing cis-regulatory motifs. Cell Reports (2012) Doi: 10.1016/j.celrep.2012.09.009 http://www.cell.com/cell-reports/fulltext/S2211-1247(12)00290-2 synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

For data on expression in imaginal discs:
Jory, A., Estella, C., Giorgianni, M.W., Slattery, M., Laverty, T.R., Rubin, G.M., and Mann, R.S. (2012) A survey of 6300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster. Cell Reports (2012) Doi: 10.1016/j.celrep.2012.09.010 http://www.cell.com/cell-reports/fulltext/S2211-1247(12)00291-4 synapse was substantially elevated, at the endocytic zone there was no enhanced polymerization activity. We conclude that actin subserves spatially diverse, independently regulated processes throughout spines. Perisynaptic actin forms a uniquely dynamic structure well suited for direct, active regulation of the synapse.

For data on expression in the larval nervous system:
Li, H.-H., Kroll, J.R., Lennox, S., Ogundeyi, O., Jeter, J., Depasquale, G., and Truman, J.W. (2013) A GAL4 driver resource for developmental and behavioral studies on the larval CNS of Drosophila. Cell Reports (submitted).

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2012.09.011}, author = {Jenett, Arnim and Rubin, Gerald M and Ngo, Teri-T B and Shepherd, David and Murphy, Christine and Dionne, Heather and Pfeiffer, Barret D and Cavallaro, Amanda and Hall, Donald and Jeter, Jennifer and Iyer, Nirmala and Fetter, Dona and Hausenfluck, Joanna H and Peng, Hanchuan and Trautman, Eric T and Svirskas, Robert R and Myers, Eugene W and Iwinski, Zbigniew R and Aso, Yoshinori and Depasquale, Gina M and Enos, Adrianne and Hulamm, Phuson and Lam, Shing Chun Benny and Li, Hsing-Hsi and Laverty, Todd R and Long, Fuhui and Qu, Lei and Murphy, Sean D and Rokicki, Konrad and Safford, Todd and Shaw, Kshiti and Simpson, Julie H and Sowell, Allison and Tae, Susana and Yu, Yang and Zugates, Christopher T} } @article {4488, title = {Generating neuronal diversity in the Drosophila central nervous system.}, journal = {Developmental Dynamics: An Official Publication of the American Association of Anatomists}, volume = {241}, year = {2012}, month = {2012 Jan}, pages = {57-68}, abstract = {

Generating diverse neurons in the central nervous system involves three major steps. First, heterogeneous neural progenitors are specified by positional cues at early embryonic stages. Second, neural progenitors sequentially produce neurons or intermediate precursors that acquire different temporal identities based on their birth-order. Third, sister neurons produced during asymmetrical terminal mitoses are given distinct fates. Determining the molecular mechanisms underlying each of these three steps of cellular diversification will unravel brain development and evolution. Drosophila has a relatively simple and tractable CNS, and previous studies on Drosophila CNS development have greatly advanced our understanding of neuron fate specification. Here we review those studies and discuss how the lessons we have learned from fly teach us the process of neuronal diversification in general.

}, issn = {1097-0177}, doi = {10.1002/dvdy.22739}, author = {Lin, Suewei and Lee, Tzumin} } @article {68815, title = {Generation of Multiple Classes of V0 Neurons in Zebrafish Spinal Cord: Progenitor Heterogeneity and Temporal Control of Neuronal Diversity}, journal = {Journal of Neuroscience}, volume = {32}, year = {2012}, month = {02/2012}, pages = {1771{\textendash}1783}, abstract = {

The developing spinal cord is subdivided into distinct progenitor domains, each of which gives rise to different types of neurons. However, the developmental mechanisms responsible for generating neuronal diversity within a domain are not well understood. Here, we have studied zebrafish V0 neurons, those that derive from the p0 progenitor domain, to address this question. We find that all V0 neurons have commissural axons, but they can be divided into excitatory and inhibitory classes. V0 excitatory neurons (V0-e) can be further categorized into three groups based on their axonal trajectories; V0-eA (ascending), V0-eB (bifurcating), and V0-eD (descending) neurons. By using time-lapse imaging of p0 progenitors and their progeny, we show that inhibitory and excitatory neurons are produced from different progenitors. We also demonstrate that V0-eA neurons are produced from distinct progenitors, while V0-eB and V0-eD neurons are produced from common progenitors. We then use birth-date analysis to reveal that V0-eA, V0-eB, and V0-eD neurons arise in this order. By perturbing Notch signaling and accelerating neuronal differentiation, we predictably alter the generation of early born V0-e neurons at the expense of later born ones. These results suggest that multiple types of V0 neurons are produced by two distinct mechanisms; from heterogeneous p0 progenitors and from the same p0 progenitor, but in a time-dependent manner.

}, issn = {0270-6474}, doi = {10.1523/JNEUROSCI.5500-11.2012}, url = {https://www.jneurosci.org/content/32/5/1771}, author = {Chie Satou and Yukiko Kimura and Shin-ichi Higashijima} } @article {6288, title = {Genetic architecture and adaptive significance of the selfing syndrome in Capsella.}, journal = {Evolution: International Journal of Organic Evolution}, volume = {66}, year = {2012}, month = {2012 May}, pages = {1360-74}, abstract = {

The transition from outcrossing to predominant self-fertilization is one of the most common evolutionary transitions in flowering plants. This shift is often accompanied by a suite of changes in floral and reproductive characters termed the selfing syndrome. Here, we characterize the genetic architecture and evolutionary forces underlying evolution of the selfing syndrome in Capsella rubella following its recent divergence from the outcrossing ancestor C. grandiflora. We conduct genotyping by multiplexed shotgun sequencing and map floral and reproductive traits in a large (N= 550) F2 population. Our results suggest that in contrast to previous studies of the selfing syndrome, changes at a few loci, some with major effects, have shaped the evolution of the selfing syndrome in Capsella. The directionality of QTL effects, as well as population genetic patterns of polymorphism and divergence at 318 loci, is consistent with a history of directional selection on the selfing syndrome. Our study is an important step toward characterizing the genetic basis and evolutionary forces underlying the evolution of the selfing syndrome in a genetically accessible model system.

}, keywords = {Biological Evolution, Capsella, Chromosome Mapping, DNA, Flowers, Genetic, Genetic Markers, Genotype, Hybridization, Multilocus Sequence Typing, Phenotype, Plant, Pollination, Polymerase Chain Reaction, Quantitative Trait Loci, Reproduction, Selection, Self-Fertilization, Self-Incompatibility in Flowering Plants, Sequence Analysis}, issn = {1558-5646}, doi = {10.1111/j.1558-5646.2011.01540.x}, author = {Slotte, Tanja and Hazzouri, Khaled M and Stern, David and Andolfatto, Peter and Wright, Stephen I} } @article {46602, title = {A genetic screen for olfactory habituation mutations in Drosophila: analysis of novel foraging alleles and an underlying neural circuit.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012 Dec 17}, pages = {e51684}, abstract = {

Habituation is a form of non-associative learning that enables animals to reduce their reaction to repeated harmless stimuli. When exposed to ethanol vapor, Drosophila show an olfactory-mediated startle response characterized by a transient increase in locomotor activity. Upon repeated exposures, this olfactory startle attenuates with the characteristics of habituation. Here we describe the results of a genetic screen to identify olfactory startle habituation (OSH) mutants. One mutation is a transcript specific allele of foraging (for) encoding a cGMP-dependent kinase. We show this allele of for reduces expression of a for-T1 isoform expressed in the head and functions normally to inhibit OSH. We localize for-T1 function to a limited set of neurons that include olfactory receptor neurons (ORNs) and the mushroom body (MB). Overexpression of for-T1 in ORNs inhibits OSH, an effect also seen upon synaptic silencing of the ORNs; for-T1 may therefore function in ORNs to decrease synaptic release upon repeated exposure to ethanol vapor. Overall, this work contributes to our understanding of the genes and neurons underlying olfactory habituation in Drosophila.

}, keywords = {Alleles, Animals, Anti-Infective Agents, Local, Cyclic GMP-Dependent Protein Kinases, Drosophila melanogaster, Drosophila Proteins, Ethanol, Genetic Testing, Habituation, Psychophysiologic, Mushroom Bodies, Mutation, Neurons, Olfactory Receptor Neurons, Reaction Time, Reflex, Startle, Smell}, issn = {1932-6203}, doi = {10.1371/journal.pone.0051684}, author = {Eddison, Mark and Belay, Amsale T and Sokolowski, Marla B and Heberlein, Ulrike} } @article {5387, title = {A genetically encoded fluorescent protein in echinoderms marks the history of neuronal activity.}, journal = {Luminescence}, volume = {27}, year = {2012}, month = {2012 Apr}, pages = {170}, abstract = {

Since the original identification of GFP from jellyfish and corals, the genetically encoded fluorescent proteins have become mainstream indicators for imaging. Functionally homologous candidates exist in more highly evolved bioluminescent invertebrates, including echinoderms. For example, in brittlestars, stimulus-evoked bioluminescence is transient, lasting seconds, and emanates from specialized cells (photocytes). Prior to light emission, we observe little or no green fluorescence. However, concurrent with light emission, an intense green, calcium-dependent fluorescence develops that persists indefinitely.

}, author = {Verdecia, Mark A. and Looger, Loren L and Lavis, Luke and Graumann, Johannes and Mandel, Gail and Brehm, Paul} } @article {4376, title = {Genetically encoded neural activity indicators.}, journal = {Current Opinion in Neurobiology}, volume = {22}, year = {2012}, month = {2012 Feb}, pages = {18-23}, abstract = {

Recording activity from identified populations of neurons is a central goal of neuroscience. Changes in membrane depolarization, particularly action potentials, are the most important features of neural physiology to extract, although ions, neurotransmitters, neuromodulators, second messengers, and the activation state of specific proteins are also crucial. Modern fluorescence microscopy provides the basis for such activity mapping, through multi-photon imaging and other optical schemes. Probes remain the rate-limiting step for progress in this field: they should be bright and photostable, and ideally come in multiple colors. Only protein-based reagents permit chronic imaging from genetically specified cells. Here we review recent progress in the design, optimization and deployment of genetically encoded indicators for calcium ions (a proxy for action potentials), membrane potential, and neurotransmitters. We highlight seminal experiments, and present an outlook for future progress.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2011.10.024}, author = {Looger, Loren L and Griesbeck, Oliver} } @article {4156, title = {Genetic manipulation of genes and cells in the nervous system of the fruit fly.}, journal = {Neuron}, volume = {72}, year = {2011}, month = {2011 Oct 20}, pages = {202-30}, abstract = {

Research in the fruit fly Drosophila melanogaster has led to insights in neural development, axon guidance, ion channel function, synaptic transmission, learning and memory, diurnal rhythmicity, and neural disease that have had broad implications for neuroscience. Drosophila is currently the eukaryotic model organism that permits the most sophisticated in\ vivo manipulations to address the function of neurons and neuronally expressed genes. Here, we summarize many of the techniques that help assess the role of specific neurons by labeling, removing, or altering their activity. We also survey genetic manipulations to identify and characterize neural genes by mutation, overexpression, and protein labeling. Here, we attempt to acquaint the reader with available options and contexts to apply these methods.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.09.021}, author = {Venken, Koen J T and Simpson, Julie H and Bellen, Hugo J} } @article {46611, title = {The genetic relationships between ethanol preference, acute ethanol sensitivity, and ethanol tolerance in Drosophila melanogaster.}, journal = {Fly (Austin)}, volume = {5}, year = {2011}, month = {2011 Jul-Sep}, pages = {191-9}, abstract = {

The relationship between alcohol consumption, sensitivity, and tolerance is an important question that has been addressed in humans and rodent models. Studies have shown that alcohol consumption and risk of abuse may correlate with (1) increased sensitivity to the stimulant effects of alcohol, (2) decreased sensitivity to the depressant effects of alcohol, and (3) increased alcohol tolerance. However, many conflicting results have been observed. To complement these studies, we utilized a different organism and approach to analyze the relationship between ethanol consumption and other ethanol responses. Using a set of 20 Drosophila melanogaster mutants that were isolated for altered ethanol sensitivity, we measured ethanol-induced hyperactivity, ethanol sedation, sedation tolerance, and ethanol consumption preference. Ethanol preference showed a strong positive correlation with ethanol tolerance, consistent with some rodent and human studies, but not with ethanol hyperactivity or sedation. No pairwise correlations were observed between ethanol hyperactivity, sedation, and tolerance. The evolutionary conservation of the relationship between tolerance and ethanol consumption in flies, rodents, and humans indicates that there are fundamental biological mechanisms linking specific ethanol responses.

}, keywords = {Alcohol Drinking, Alcoholic Intoxication, Animals, Central Nervous System Depressants, Drosophila melanogaster, Drosophila Proteins, Ethanol, Food Preferences, Hyperkinesis, Male, Transcription Factors}, issn = {1933-6942}, author = {Devineni, Anita V and McClure, Kimberly D and Guarnieri, Douglas J and Corl, Ammon B and Wolf, Fred W and Eddison, Mark and Heberlein, Ulrike} } @article {4371, title = {A genetically encoded, high-signal-to-noise maltose sensor.}, journal = {Proteins}, volume = {79}, year = {2011}, month = {2011 Nov}, pages = {3025-36}, abstract = {

We describe the generation of a family of high-signal-to-noise single-wavelength genetically encoded indicators for maltose. This was achieved by insertion of circularly permuted fluorescent proteins into a bacterial periplasmic binding protein (PBP), Escherichia coli maltodextrin-binding protein, resulting in a four-color family of maltose indicators. The sensors were iteratively optimized to have sufficient brightness and maltose-dependent fluorescence increases for imaging, under both one- and two-photon illumination. We demonstrate that maltose affinity of the sensors can be tuned in a fashion largely independent of the fluorescent readout mechanism. Using literature mutations, the binding specificity could be altered to moderate sucrose preference, but with a significant loss of affinity. We use the soluble sensors in individual E. coli bacteria to observe rapid maltose transport across the plasma membrane, and membrane fusion versions of the sensors on mammalian cells to visualize the addition of maltose to extracellular media. The PBP superfamily includes scaffolds specific for a number of analytes whose visualization would be critical to the reverse engineering of complex systems such as neural networks, biosynthetic pathways, and signal transduction cascades. We expect the methodology outlined here to be useful in the development of indicators for many such analytes.

}, issn = {1097-0134}, doi = {10.1002/prot.23118}, author = {Marvin, Jonathan S and Schreiter, Eric R and Echevarr{\'\i}a, Ileabett M and Looger, Loren L} } @article {46613, title = {Genome-wide association and genetic functional studies identify autism susceptibility candidate 2 gene (AUTS2) in the regulation of alcohol consumption.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Apr 26}, pages = {7119-24}, abstract = {

Alcohol consumption is a moderately heritable trait, but the genetic basis in humans is largely unknown, despite its clinical and societal importance. We report a genome-wide association study meta-analysis of \~{}2.5 million directly genotyped or imputed SNPs with alcohol consumption (gram per day per kilogram body weight) among 12 population-based samples of European ancestry, comprising 26,316 individuals, with replication genotyping in an additional 21,185 individuals. SNP rs6943555 in autism susceptibility candidate 2 gene (AUTS2) was associated with alcohol consumption at genome-wide significance (P = 4 {\texttimes} 10(-8) to P = 4 {\texttimes} 10(-9)). We found a genotype-specific expression of AUTS2 in 96 human prefrontal cortex samples (P = 0.026) and significant (P \< 0.017) differences in expression of AUTS2 in whole-brain extracts of mice selected for differences in voluntary alcohol consumption. Down-regulation of an AUTS2 homolog caused reduced alcohol sensitivity in Drosophila (P \< 0.001). Our finding of a regulator of alcohol consumption adds knowledge to our understanding of genetic mechanisms influencing alcohol drinking behavior.

}, keywords = {Alcohol Drinking, Animals, Drosophila melanogaster, European Continental Ancestry Group, Female, Gene Expression Regulation, Genome-Wide Association Study, Genotype, Humans, Male, Mice, Nuclear Proteins, Polymorphism, Single Nucleotide, Proteins, Quantitative Trait, Heritable}, issn = {1091-6490}, doi = {10.1073/pnas.1017288108}, author = {Schumann, Gunter and Coin, Lachlan J and Lourdusamy, Anbarasu and Charoen, Pimphen and Berger, Karen H and Stacey, David and Desrivi{\`e}res, Sylvane and Aliev, Fazil A and Khan, Anokhi A and Amin, Najaf and Aulchenko, Yurii S and Bakalkin, Georgy and Bakker, Stephan J and Balkau, Beverley and Beulens, Joline W and Bilbao, Ainhoa and de Boer, Rudolf A and Beury, Delphine and Bots, Michiel L and Breetvelt, Elemi J and Cauchi, St{\'e}phane and Cavalcanti-Proen{\c c}a, Christine and Chambers, John C and Clarke, Toni-Kim and Dahmen, Norbert and de Geus, Eco J and Dick, Danielle and Ducci, Francesca and Easton, Alanna and Edenberg, Howard J and Esko, T{\~o}nu and Esk, T{\~o}nu and Fern{\'a}ndez-Medarde, Alberto and Foroud, Tatiana and Freimer, Nelson B and Girault, Jean-Antoine and Grobbee, Diederick E and Guarrera, Simonetta and Gudbjartsson, Daniel F and Hartikainen, Anna-Liisa and Heath, Andrew C and Hesselbrock, Victor and Hofman, Albert and Hottenga, Jouke-Jan and Isohanni, Matti K and Kaprio, Jaakko and Khaw, Kay-Tee and Kuehnel, Brigitte and Laitinen, Jaana and Lobbens, St{\'e}phane and Luan, Jian{\textquoteright}an and Mangino, Massimo and Maroteaux, Matthieu and Matullo, Giuseppe and McCarthy, Mark I and Mueller, Christian and Navis, Gerjan and Numans, Mattijs E and N{\'u}{\~n}ez, Alejandro and Nyholt, Dale R and Onland-Moret, Charlotte N and Oostra, Ben A and O{\textquoteright}Reilly, Paul F and Palkovits, Miklos and Penninx, Brenda W and Polidoro, Silvia and Pouta, Anneli and Prokopenko, Inga and Ricceri, Fulvio and Santos, Eugenio and Smit, Johannes H and Soranzo, Nicole and Song, Kijoung and Sovio, Ulla and Stumvoll, Michael and Surakk, Ida and Thorgeirsson, Thorgeir E and Thorsteinsdottir, Unnur and Troakes, Claire and Tyrfingsson, Thorarinn and T{\"o}njes, Anke and Uiterwaal, Cuno S and Uitterlinden, Andre G and van der Harst, Pim and van der Schouw, Yvonne T and Staehlin, Oliver and Vogelzangs, Nicole and Vollenweider, Peter and Waeber, Gerard and Wareham, Nicholas J and Waterworth, Dawn M and Whitfield, John B and Wichmann, Erich H and Willemsen, Gonneke and Witteman, Jacqueline C and Yuan, Xin and Zhai, Guangju and Zhao, Jing H and Zhang, Weihua and Martin, Nicholas G and Metspalu, Andres and Doering, Angela and Scott, James and Spector, Tim D and Loos, Ruth J and Boomsma, Dorret I and Mooser, Vincent and Peltonen, Leena and Stefansson, Kari and van Duijn, Cornelia M and Vineis, Paolo and Sommer, Wolfgang H and Kooner, Jaspal S and Spanagel, Rainer and Heberlein, Ulrike A and Jarvelin, Marjo-Riitta and Elliott, Paul} } @article {4300, title = {Glia instruct developmental neuronal remodeling through TGF-β signaling.}, journal = {Nature Neuroscience}, volume = {14}, year = {2011}, month = {2011 Jun 19}, pages = {821-3}, abstract = {

We found that glia secrete myoglianin, a TGF-β ligand, to instruct developmental neural remodeling in Drosophila. Glial myoglianin upregulated neuronal expression of an ecdysone nuclear receptor that triggered neurite remodeling following the late-larval ecdysone peak. Thus glia orchestrate developmental neural remodeling not only by engulfment of unwanted neurites but also by enabling neuron remodeling.

}, keywords = {Animals, Developmental, Double-Stranded, Drosophila, Drosophila Proteins, Gene Expression Regulation, Genetically Modified, Green Fluorescent Proteins, MicroRNAs, Models, Mushroom Bodies, Mutation, Neurogenesis, Neuroglia, Neurological, RNA, Signal Transduction, Transforming Growth Factor beta}, issn = {1546-1726}, doi = {10.1038/nn.2833}, author = {Awasaki, Takeshi and Huang, Yaling and O{\textquoteright}Connor, Michael B and Lee, Tzumin} } @article {46425, title = {Glial-derived prodegenerative signaling in the Drosophila neuromuscular system.}, journal = {Neuron}, volume = {72}, year = {2011}, month = {2011 Dec 8}, pages = {760-75}, abstract = {

We provide evidence for a prodegenerative, glial-derived signaling framework in the Drosophila neuromuscular system that includes caspase and mitochondria-dependent signaling. We demonstrate that Drosophila TNF-α (eiger) is expressed in a subset of peripheral glia, and the TNF-α receptor (TNFR), Wengen, is expressed in motoneurons. NMJ degeneration caused by disruption of the spectrin/ankyrin skeleton is suppressed by an eiger mutation or by eiger knockdown within a subset of peripheral glia. Loss of wengen in motoneurons causes a similar suppression providing evidence for glial-derived prodegenerative TNF-α signaling. Neither JNK nor NFκβ is required for prodegenerative signaling. However, we provide evidence for the involvement of both an initiator and effector caspase, Dronc and Dcp-1, and mitochondrial-dependent signaling. Mutations that deplete the axon and nerve terminal of mitochondria suppress degeneration as do mutations in Drosophila Bcl-2 (debcl), a mitochondria-associated protein, and Apaf-1 (dark), which links mitochondrial signaling with caspase activity in other systems.

}, keywords = {Animals, Animals, Genetically Modified, Apoptotic Protease-Activating Factor 1, Caspases, Disease Models, Animal, Drosophila, Drosophila Proteins, Excitatory Postsynaptic Potentials, Fluorescence Recovery After Photobleaching, Green Fluorescent Proteins, Mitochondria, Motor Neuron Disease, Mutation, Nerve Degeneration, Nerve Tissue Proteins, Neuroglia, Neuromuscular Junction, Proto-Oncogene Proteins, Receptors, Tumor Necrosis Factor, RNA Interference, Signal Transduction}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.09.031}, author = {Keller, Lani C and Cheng, Ling and Locke, Cody J and M{\"u}ller, Martin and Fetter, Richard D and Davis, Graeme W} } @article {4385, title = {A gustotopic map of taste qualities in the mammalian brain.}, journal = {Science}, volume = {333}, year = {2011}, month = {2011 Sep 2}, pages = {1262-6}, abstract = {

The taste system is one of our fundamental senses, responsible for detecting and responding to sweet, bitter, umami, salty, and sour stimuli. In the tongue, the five basic tastes are mediated by separate classes of taste receptor cells each finely tuned to a single taste quality. We explored the logic of taste coding in the brain by examining how sweet, bitter, umami, and salty qualities are represented in the primary taste cortex of mice. We used in vivo two-photon calcium imaging to demonstrate topographic segregation in the functional architecture of the gustatory cortex. Each taste quality is represented in its own separate cortical field, revealing the existence of a gustotopic map in the brain. These results expose the basic logic for the central representation of taste.

}, keywords = {Afferent Pathways, Animals, Brain Mapping, Cerebral Cortex, Cycloheximide, Inbred C57BL, Knockout, Mice, Molecular Imaging, Neurons, Sodium Chloride, Sodium Glutamate, Sweetening Agents, Taste, Taste Buds}, issn = {1095-9203}, doi = {10.1126/science.1204076}, author = {Chen, Xiaoke and Gabitto, Mariano and Peng, Yueqing and Ryba, Nicholas J P and Zuker, Charles S} } @article {4402, title = {Genome sequence of the pea aphid Acyrthosiphon pisum.}, journal = {PLoS Biology}, volume = {8}, year = {2010}, month = {2010 Feb}, pages = {e1000313}, abstract = {

Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.

}, keywords = {Animals, Aphids, Buchnera, Gene Transfer, Genome, Horizontal, Insect, Symbiosis}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1000313} } @article {6338, title = {GPU-enabled FREALIGN: accelerating single particle 3D reconstruction and refinement in Fourier space on graphics processors.}, journal = {Journal of Structural Biology}, volume = {172}, year = {2010}, month = {2010 Dec}, pages = {407-12}, abstract = {

Among all the factors that determine the resolution of a 3D reconstruction by single particle electron cryo-microscopy (cryoEM), the number of particle images used in the dataset plays a major role. More images generally yield better resolution, assuming the imaged protein complex is conformationally and compositionally homogeneous. To facilitate processing of very large datasets, we modified the computer program, FREALIGN, to execute the computationally most intensive procedures on Graphics Processing Units (GPUs). Using the modified program, the execution speed increased between 10 and 240-fold depending on the task performed by FREALIGN. Here we report the steps necessary to parallelize critical FREALIGN subroutines and evaluate its performance on computers with multiple GPUs.

}, keywords = {Computer-Assisted, Cryoelectron Microscopy, Image Processing, Imaging, Three-Dimensional}, issn = {1095-8657}, doi = {10.1016/j.jsb.2010.06.010}, author = {Li, Xueming and Grigorieff, Nikolaus and Cheng, Yifan} } @article {46621, title = {Genetic aspects of behavioral neurotoxicology.}, journal = {Neurotoxicology}, volume = {30}, year = {2009}, month = {2009 Sep}, pages = {741-53}, abstract = {

Considerable progress has been made over the past couple of decades concerning the molecular bases of neurobehavioral function and dysfunction. The field of neurobehavioral genetics is becoming mature. Genetic factors contributing to neurologic diseases such as Alzheimer{\textquoteright}s disease have been found and evidence for genetic factors contributing to other diseases such as schizophrenia and autism are likely. This genetic approach can also benefit the field of behavioral neurotoxicology. It is clear that there is substantial heterogeneity of response with behavioral impairments resulting from neurotoxicants. Many factors contribute to differential sensitivity, but it is likely that genetic variability plays a prominent role. Important discoveries concerning genetics and behavioral neurotoxicity are being made on a broad front from work with invertebrate and piscine mutant models to classic mouse knockout models and human epidemiologic studies of polymorphisms. Discovering genetic factors of susceptibility to neurobehavioral toxicity not only helps identify those at special risk, it also advances our understanding of the mechanisms by which toxicants impair neurobehavioral function in the larger population. This symposium organized by Edward Levin and Annette Kirshner, brought together researchers from the laboratories of Michael Aschner, Douglas Ruden, Ulrike Heberlein, Edward Levin and Kathleen Welsh-Bohmer conducting studies with Caenorhabditis elegans, Drosophila, fish, rodents and humans studies to determine the role of genetic factors in susceptibility to behavioral impairment from neurotoxic exposure.

}, keywords = {Animals, Behavior, Disease Models, Animal, Genetics, Humans, Neurotoxicity Syndromes, Neurotoxins, Phylogeny, Toxicology}, issn = {1872-9711}, doi = {10.1016/j.neuro.2009.07.014}, author = {Levin, Edward D and Aschner, Michael and Heberlein, Ulrike and Ruden, Douglas and Welsh-Bohmer, Kathleen A and Bartlett, Selena and Berger, Karen and Chen, Lang and Corl, Ammon B and Eddins, Donnie and French, Rachael and Hayden, Kathleen M and Helmcke, Kirsten and Hirsch, Helmut V B and Linney, Elwood and Lnenicka, Greg and Page, Grier P and Possidente, Debra and Possidente, Bernard and Kirshner, Annette} } @article {3566, title = {Is genetic evolution predictable?}, journal = {Science}, volume = {323}, year = {2009}, month = {2009 Feb 6}, pages = {746-51}, abstract = {

Ever since the integration of Mendelian genetics into evolutionary biology in the early 20th century, evolutionary geneticists have for the most part treated genes and mutations as generic entities. However, recent observations indicate that all genes are not equal in the eyes of evolution. Evolutionarily relevant mutations tend to accumulate in hotspot genes and at specific positions within genes. Genetic evolution is constrained by gene function, the structure of genetic networks, and population biology. The genetic basis of evolution may be predictable to some extent, and further understanding of this predictability requires incorporation of the specific functions and characteristics of genes into evolutionary theory.

}, keywords = {Animals, Arabidopsis, Biological Evolution, Drosophila, Epistasis, Evolution, Gene Regulatory Networks, Genes, Genetic, Genetic Speciation, Genetic Variation, Molecular, Mutation, Phenotype, Plants, Population Dynamics, Selection}, issn = {1095-9203}, doi = {10.1126/science.1158997}, author = {Stern, David L and Orgogozo, Virginie} } @article {46786, title = {Globally optimal stitching of tiled 3D microscopic image acquisitions.}, journal = {Bioinformatics}, volume = {25}, year = {2009}, month = {2009 Jun 1}, pages = {1463-5}, abstract = {

MOTIVATION: Modern anatomical and developmental studies often require high-resolution imaging of large specimens in three dimensions (3D). Confocal microscopy produces high-resolution 3D images, but is limited by a relatively small field of view compared with the size of large biological specimens. Therefore, motorized stages that move the sample are used to create a tiled scan of the whole specimen. The physical coordinates provided by the microscope stage are not precise enough to allow direct reconstruction (Stitching) of the whole image from individual image stacks.

RESULTS: To optimally stitch a large collection of 3D confocal images, we developed a method that, based on the Fourier Shift Theorem, computes all possible translations between pairs of 3D images, yielding the best overlap in terms of the cross-correlation measure and subsequently finds the globally optimal configuration of the whole group of 3D images. This method avoids the propagation of errors by consecutive registration steps. Additionally, to compensate the brightness differences between tiles, we apply a smooth, non-linear intensity transition between the overlapping images. Our stitching approach is fast, works on 2D and 3D images, and for small image sets does not require prior knowledge about the tile configuration.

AVAILABILITY: The implementation of this method is available as an ImageJ plugin distributed as a part of the Fiji project (Fiji is just ImageJ: http://pacific.mpi-cbg.de/).

}, keywords = {Animals, Drosophila, Imaging, Three-Dimensional, Larva, Microscopy, Confocal}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btp184}, author = {Preibisch, Stephan and Saalfeld, Stephan and Tomancak, Pavel} } @article {5485, title = {Glycogen synthase kinase-3/Shaggy mediates ethanol-induced excitotoxic cell death of Drosophila olfactory neurons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, year = {2009}, month = {2009 Dec 8}, pages = {20924-9}, abstract = {

It has long been known that heavy alcohol consumption leads to neuropathology and neuronal death. While the response of neurons to an ethanol insult is strongly influenced by genetic background, the underlying mechanisms are poorly understood. Here, we show that even a single intoxicating exposure to ethanol causes non-cell-autonomous apoptotic death specifically of Drosophila olfactory neurons, which is accompanied by a loss of a behavioral response to the smell of ethanol and a blackening of the third antennal segment. The Drosophila homolog of glycogen synthase kinase-3 (GSK-3)beta, Shaggy, is required for ethanol-induced apoptosis. Consistent with this requirement, the GSK-3beta inhibitor lithium protects against the neurotoxic effects of ethanol, indicating the possibility for pharmacological intervention in cases of alcohol-induced neurodegeneration. Ethanol-induced death of olfactory neurons requires both their neural activity and functional NMDA receptors. This system will allow the investigation of the genetic and molecular basis of ethanol-induced apoptosis in general and provide an understanding of the molecular role of GSK-3beta in programmed cell death.

}, keywords = {Amino Acid, Animals, Cell Death, Drosophila melanogaster, Drosophila Proteins, Electricity, Ethanol, Gene Silencing, Glycogen Synthase Kinase 3, Lithium, N-Methyl-D-Aspartate, Neurotoxins, Olfactory Receptor Neurons, Receptors, Sequence Homology, Volatilization}, issn = {1091-6490}, doi = {10.1073/pnas.0910813106}, author = {French, Rachael L and Heberlein, Ulrike} } @article {4257, title = {Genetic dissection of neural circuits.}, journal = {Neuron}, volume = {57}, year = {2008}, month = {2008 Mar 13}, pages = {634-60}, abstract = {

Understanding the principles of information processing in neural circuits requires systematic characterization of the participating cell types and their connections, and the ability to measure and perturb their activity. Genetic approaches promise to bring experimental access to complex neural systems, including genetic stalwarts such as the fly and mouse, but also to nongenetic systems such as primates. Together with anatomical and physiological methods, cell-type-specific expression of protein markers and sensors and transducers will be critical to construct circuit diagrams and to measure the activity of genetically defined neurons. Inactivation and activation of genetically defined cell types will establish causal relationships between activity in specific groups of neurons, circuit function, and animal behavior. Genetic analysis thus promises to reveal the logic of the neural circuits in complex brains that guide behaviors. Here we review progress in the genetic analysis of neural circuits and discuss directions for future research and development.

}, keywords = {Animals, Gene Expression Regulation, Humans, Nerve Net, Neural Pathways, Neurons}, issn = {1097-4199}, doi = {10.1016/j.neuron.2008.01.002}, author = {Luo, Liqun and Callaway, Edward M and Svoboda, Karel} } @article {46625, title = {Genetic dissociation of ethanol sensitivity and memory formation in Drosophila melanogaster.}, journal = {Genetics}, volume = {178}, year = {2008}, month = {2008 Apr}, pages = {1895-902}, abstract = {

The ad hoc genetic correlation between ethanol sensitivity and learning mechanisms in Drosophila could overemphasize a common process supporting both behaviors. To challenge directly the hypothesis that these mechanisms are singular, we examined the learning phenotypes of 10 new strains. Five of these have increased ethanol sensitivity, and the other 5 do not. We tested place and olfactory memory in each of these lines and found two new learning mutations. In one case, altering the tribbles gene, flies have a significantly reduced place memory, elevated olfactory memory, and normal ethanol response. In the second case, mutation of a gene we name ethanol sensitive with low memory (elm), place memory was not altered, olfactory memory was sharply reduced, and sensitivity to ethanol was increased. In sum, however, we found no overall correlation between ethanol sensitivity and place memory in the 10 lines tested. Furthermore, there was a weak but nonsignificant correlation between ethanol sensitivity and olfactory learning. Thus, mutations that alter learning and sensitivity to ethanol can occur independently of each other and this implies that the set of genes important for both ethanol sensitivity and learning is likely a subset of the genes important for either process.

}, keywords = {Animals, Behavior, Animal, Cell Cycle Proteins, DNA Transposable Elements, Drosophila melanogaster, Drosophila Proteins, Ethanol, Gene Expression Regulation, Head, Memory, Mutagenesis, Insertional, Phenotype, Protein-Serine-Threonine Kinases, RNA, Messenger}, issn = {0016-6731}, doi = {10.1534/genetics.107.084582}, author = {LaFerriere, Holly and Guarnieri, Douglas J and Sitaraman, Divya and Diegelmann, Soeren and Heberlein, Ulrike and Zars, Troy} } @article {4254, title = {A genetically encoded fluorescent sensor of ERK activity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, year = {2008}, month = {2008 Dec 9}, pages = {19264-9}, abstract = {

The activity of the ERK has complex spatial and temporal dynamics that are important for the specificity of downstream effects. However, current biochemical techniques do not allow for the measurement of ERK signaling with fine spatiotemporal resolution. We developed a genetically encoded, FRET-based sensor of ERK activity (the extracellular signal-regulated kinase activity reporter, EKAR), optimized for signal-to-noise ratio and fluorescence lifetime imaging. EKAR selectively and reversibly reported ERK activation in HEK293 cells after epidermal growth factor stimulation. EKAR signals were correlated with ERK phosphorylation, required ERK activity, and did not report the activities of JNK or p38. EKAR reported ERK activation in the dendrites and nucleus of hippocampal pyramidal neurons in brain slices after theta-burst stimuli or trains of back-propagating action potentials. EKAR therefore permits the measurement of spatiotemporal ERK signaling dynamics in living cells, including in neuronal compartments in intact tissues.

}, keywords = {Action Potentials, Animals, Artifacts, Bacterial Proteins, Cell Line, Dendrites, Endothelial Cells, Enzyme Activation, Extracellular Signal-Regulated MAP Kinases, Fluorescence Resonance Energy Transfer, Fluorescent Dyes, Genes, Green Fluorescent Proteins, Hippocampus, Humans, Kidney, Luminescent Proteins, MAP Kinase Signaling System, Organ Culture Techniques, Patch-Clamp Techniques, Pyramidal Cells, Rats, Reporter}, issn = {1091-6490}, doi = {10.1073/pnas.0804598105}, author = {Harvey, Christopher D and Ehrhardt, Anka G and Cellurale, Cristina and Zhong, Haining and Yasuda, Ryohei and Davis, Roger J and Svoboda, Karel} } @article {3932, title = {Genetically encoded fluorescent sensors for studying healthy and diseased nervous systems.}, journal = {Drug Discovery Today. Disease Models}, volume = {5}, year = {2008}, month = {2008}, pages = {27-35}, abstract = {

Neurons and glia are functionally organized into circuits and higher-order structures via synaptic connectivity, well-orchestrated molecular signaling, and activity-dependent refinement. Such organization allows the precise information processing required for complex behaviors. Disruption of nervous systems by genetic deficiency or events such as trauma or environmental exposure may produce a diseased state in which certain aspects of inter-neuron signaling are impaired. Optical imaging techniques allow the direct visualization of individual neurons in a circuit environment. Imaging probes specific for given biomolecules may help elucidate their contribution to proper circuit function. Genetically encoded sensors can visualize trafficking of particular molecules in defined neuronal populations, non-invasively in intact brain or reduced preparations. Sensor analysis in healthy and diseased brains may reveal important differences and shed light on the development and progression of nervous system disorders. We review the field of genetically encoded sensors for molecules and cellular events, and their potential applicability to the study of nervous system disease.

}, issn = {1740-6757}, doi = {10.1016/j.ddmod.2008.07.003}, author = {Tian, Lin and Looger, Loren L} } @article {2679, title = {Genomic analysis of Drosophila neuronal remodeling: a role for the RNA-binding protein Boule as a negative regulator of axon pruning.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {28}, year = {2008}, month = {2008 Jun 11}, pages = {6092-103}, abstract = {

Drosophila mushroom body (MB) gamma neurons undergo axon pruning during metamorphosis through a process of localized degeneration of specific axon branches. Developmental axon degeneration is initiated by the steroid hormone ecdysone, acting through a nuclear receptor complex composed of USP (ultraspiracle) and EcRB1 (ecdysone receptor B1) to regulate gene expression in MB gamma neurons. To identify ecdysone-dependent gene expression changes in MB gamma neurons at the onset of axon pruning, we use laser capture microdissection to isolate wild-type and mutant MB neurons in which EcR (ecdysone receptor) activity is genetically blocked, and analyze expression changes by microarray. We identify several molecular pathways that are regulated in MB neurons by ecdysone. The most striking observation is the upregulation of genes involved in the UPS (ubiquitin-proteasome system), which is cell autonomously required for gamma neuron pruning. In addition, we characterize the function of Boule, an evolutionarily conserved RNA-binding protein previously implicated in spermatogenesis in flies and vertebrates. boule expression is downregulated by ecdysone in MB neurons at the onset of pruning, and forced expression of Boule in MB gamma neurons is sufficient to inhibit axon pruning. This activity is dependent on the RNA-binding domain of Boule and a conserved DAZ (deleted in azoospermia) domain implicated in interactions with other RNA-binding proteins. However, loss of Boule does not result in obvious defects in axon pruning or morphogenesis of MB neurons, suggesting that it acts redundantly with other ecdyonse-regulated genes. We propose a novel function for Boule in the CNS as a negative regulator of developmental axon pruning.

}, keywords = {Animals, Antigens, Axons, CD8, Developmental, Drosophila, Drosophila Proteins, Ecdysone, Gene Expression Regulation, Genetically Modified, Genomics, Green Fluorescent Proteins, Larva, Microarray Analysis, Mushroom Bodies, Mutation, Neurons, Receptors, RNA-Binding Proteins, Steroid}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0677-08.2008}, author = {Hoopfer, Eric D and Penton, Andrea and Watts, Ryan J and Luo, Liqun} } @article {6502, title = {GFP Reconstitution Across Synaptic Partners (GRASP) defines cell contacts and synapses in living nervous systems.}, journal = {Neuron}, volume = {57}, year = {2008}, month = {2008 Feb 7}, pages = {353-63}, abstract = {

The identification of synaptic partners is challenging in dense nerve bundles, where many processes occupy regions beneath the resolution of conventional light microscopy. To address this difficulty, we have developed GRASP, a system to label membrane contacts and synapses between two cells in living animals. Two complementary fragments of GFP are expressed on different cells, tethered to extracellular domains of transmembrane carrier proteins. When the complementary GFP fragments are fused to ubiquitous transmembrane proteins, GFP fluorescence appears uniformly along membrane contacts between the two cells. When one or both GFP fragments are fused to synaptic transmembrane proteins, GFP fluorescence is tightly localized to synapses. GRASP marks known synaptic contacts in C. elegans, correctly identifies changes in mutants with altered synaptic specificity, and can uncover new information about synaptic locations as confirmed by electron microscopy. GRASP may prove particularly useful for defining connectivity in complex nervous systems.

}, keywords = {Animal, Animals, Behavior, Biological, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Carrier Proteins, Cells, Cultured, Electron, Genetically Modified, Green Fluorescent Proteins, Microscopy, Models, Mutation, Nervous System, Neurons, Synapses}, issn = {0896-6273}, doi = {10.1016/j.neuron.2007.11.030}, author = {Feinberg, Evan H and Vanhoven, Miri K and Bendesky, Andres and Wang, George and Fetter, Richard D and Shen, Kang and Bargmann, Cornelia I} } @proceedings {45799, title = {Gene expression patterns underlying wing polyphenism and polymorphism in the pea aphid}, volume = {46}, year = {2007}, month = {01/2007}, pages = {E186-E186}, publisher = {OXFORD UNIV PRESS INC}, abstract = {

The pea aphid, Acyrthosiphon pisum, exhibits several environmentally cued, discrete, alternate phenotypes (polyphenisms) during its life cycle. In the wing polyphenism, female progeny develop as either winged or unwinged depending on the extent of crowding or host plant quality experienced by the mother. Males also have the ability to develop as either winged or unwinged, but this is genetically determined by a single locus on the X chromosome and is thus referred to as a wing polymorphism. In order to gain insight into the patterns of gene expression that underlie the wing polyphenism and polymorphism we have used a pea aphid cDNA microarray to examine gene expression in winged and unwinged females and males. Results suggest that winged and unwinged morphs exhibit systemic differences in gene expression and that many of these differences are shared between the wing polyphenism and polymorphism (i.e., between females and males). In addition, adult winged and unwinged males exhibit pronounced differences when compared to adult females and fourth instar males, as well as to each other.

}, url = {http://www.sicb.org/meetings/2007/schedule/abstractdetails.php3?id=649}, author = {GK Davis and JA Brisson and DL Stern} } @article {1290, title = {Genome-wide screen for modifiers of ataxin-3 neurodegeneration in Drosophila.}, journal = {PLoS Genetics}, volume = {3}, year = {2007}, month = {2007 Oct 19}, pages = {1950-64}, abstract = {

Spinocerebellar ataxia type-3 (SCA3) is among the most common dominantly inherited ataxias, and is one of nine devastating human neurodegenerative diseases caused by the expansion of a CAG repeat encoding glutamine within the gene. The polyglutamine domain confers toxicity on the protein Ataxin-3 leading to neuronal dysfunction and loss. Although modifiers of polyglutamine toxicity have been identified, little is known concerning how the modifiers function mechanistically to affect toxicity. To reveal insight into spinocerebellar ataxia type-3, we performed a genetic screen in Drosophila with pathogenic Ataxin-3-induced neurodegeneration and identified 25 modifiers defining 18 genes. Despite a variety of predicted molecular activities, biological analysis indicated that the modifiers affected protein misfolding. Detailed mechanistic studies revealed that some modifiers affected protein accumulation in a manner dependent on the proteasome, whereas others affected autophagy. Select modifiers of Ataxin-3 also affected tau, revealing common pathways between degeneration due to distinct human neurotoxic proteins. These findings provide new insight into molecular pathways of polyQ toxicity, defining novel targets for promoting neuronal survival in human neurodegenerative disease.

}, keywords = {Animals, Crosses, Drosophila melanogaster, Genetic, Genome, Humans, Models, Nerve Tissue Proteins, Neurodegenerative Diseases, Neurons, Nuclear Proteins, Peptides, Phagocytosis, Proteasome Endopeptidase Complex, Protein Denaturation, Protein Folding, Repressor Proteins, Ubiquitin}, issn = {1553-7404}, doi = {10.1371/journal.pgen.0030177}, author = {Bilen, Julide and Bonini, Nancy M} } @article {6857, title = {A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila.}, journal = {Nature}, volume = {448}, year = {2007}, month = {2007 Jul 12}, pages = {151-6}, abstract = {

Forward genetic screens in model organisms have provided important insights into numerous aspects of development, physiology and pathology. With the availability of complete genome sequences and the introduction of RNA-mediated gene interference (RNAi), systematic reverse genetic screens are now also possible. Until now, such genome-wide RNAi screens have mostly been restricted to cultured cells and ubiquitous gene inactivation in Caenorhabditis elegans. This powerful approach has not yet been applied in a tissue-specific manner. Here we report the generation and validation of a genome-wide library of Drosophila melanogaster RNAi transgenes, enabling the conditional inactivation of gene function in specific tissues of the intact organism. Our RNAi transgenes consist of short gene fragments cloned as inverted repeats and expressed using the binary GAL4/UAS system. We generated 22,270 transgenic lines, covering 88\% of the predicted protein-coding genes in the Drosophila genome. Molecular and phenotypic assays indicate that the majority of these transgenes are functional. Our transgenic RNAi library thus opens up the prospect of systematically analysing gene functions in any tissue and at any stage of the Drosophila lifespan.

}, keywords = {Animals, Drosophila melanogaster, Exons, Female, Genetically Modified, Genomic Library, Male, Messenger, Muscles, Neurons, Organ Specificity, Ribonuclease III, RNA, RNA Interference}, issn = {1476-4687}, doi = {10.1038/nature05954}, author = {Dietzl, Georg and Chen, Doris and Schnorrer, Frank and Su, Kuan-Chung and Barinova, Yulia and Fellner, Michaela and Gasser, Beate and Kinsey, Kaolin and Oppel, Silvia and Scheiblauer, Susanne and Couto, Africa and Marra, Vincent and Keleman, Krystyna and Dickson, Barry J} } @article {6249, title = {Global analyses of mRNA translational control during early Drosophila embryogenesis.}, journal = {Genome Biology}, volume = {8}, year = {2007}, month = {2007}, pages = {R63}, abstract = {

BACKGROUND: In many animals, the first few hours of life proceed with little or no transcription, and developmental regulation at these early stages is dependent on maternal cytoplasm rather than the zygotic nucleus. Translational control is critical for early Drosophila embryogenesis and is exerted mainly at the gene level. To understand post-transcriptional regulation during Drosophila early embryonic development, we used sucrose polysomal gradient analyses and GeneChip analysis to illustrate the translation profile of individual mRNAs. RESULTS: We determined ribosomal density and ribosomal occupancy of over 10,000 transcripts during the first ten hours after egg laying. CONCLUSION: We report the extent and general nature of gene regulation at the translational level during early Drosophila embryogenesis on a genome-wide basis. The diversity of the translation profiles indicates multiple mechanisms modulating transcript-specific translation. Cluster analyses suggest that the genes involved in some biological processes are co-regulated at the translational level at certain developmental stages.

}, keywords = {Animals, Cluster Analysis, Developmental, Drosophila, Embryo, Embryonic Development, Gene Expression Regulation, Messenger, Nonmammalian, Polyribosomes, Protein Biosynthesis, Ribosomes, RNA, RNA 5{\textquoteright} Terminal Oligopyrimidine Sequence}, issn = {1465-6914}, doi = {10.1186/gb-2007-8-4-r63}, author = {Qin, Xiaoli and Ahn, Soyeon and Speed, Terence P and Rubin, Gerald M} } @article {955, title = {Global analysis of patterns of gene expression during Drosophila embryogenesis.}, journal = {Genome Biology}, volume = {8}, year = {2007}, month = {2007 July 23}, pages = {R145}, abstract = {

Cell and tissue specific gene expression is a defining feature of embryonic development in multi-cellular organisms. However, the range of gene expression patterns, the extent of the correlation of expression with function, and the classes of genes whose spatial expression are tightly regulated have been unclear due to the lack of an unbiased, genome-wide survey of gene expression patterns.

}, keywords = {Animals, Drosophila melanogaster, Embryonic Development, Gene Expression Profiling}, issn = {1465-6914}, doi = {10.1186/gb-2007-8-7-r145}, author = {Tomancak, Pavel and Berman, Benjamin P and Beaton, Amy and Weiszmann, Richard and Kwan, Elaine and Hartenstein, Volker and Celniker, Susan E and Rubin, Gerald M} } @article {1582, title = {A global transcriptional regulator in Thermococcus kodakaraensis controls the expression levels of both glycolytic and gluconeogenic enzyme-encoding genes.}, journal = {The Journal of Biological Chemistry}, volume = {282}, year = {2007}, month = {2007 Nov 16}, pages = {33659-70}, abstract = {

We identified a novel regulator, Thermococcales glycolytic regulator (Tgr), functioning as both an activator and a repressor of transcription in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. Tgr (TK1769) displays similarity (28\% identical) to Pyrococcus furiosus TrmB (PF1743), a transcriptional repressor regulating the trehalose/maltose ATP-binding cassette transporter genes, but is more closely related (67\%) to a TrmB paralog in P. furiosus (PF0124). Growth of a tgr disruption strain (Deltatgr) displayed a significant decrease in growth rate under gluconeogenic conditions compared with the wild-type strain, whereas comparable growth rates were observed under glycolytic conditions. A whole genome microarray analysis revealed that transcript levels of almost all genes related to glycolysis and maltodextrin metabolism were at relatively high levels in the Deltatgr mutant even under gluconeogenic conditions. The Deltatgr mutant also displayed defects in the transcriptional activation of gluconeogenic genes under these conditions, indicating that Tgr functions as both an activator and a repressor. Genes regulated by Tgr contain a previously identified sequence motif, the Thermococcales glycolytic motif (TGM). The TGM was positioned upstream of the Transcription factor B-responsive element (BRE)/TATA sequence in gluconeogenic promoters and downstream of it in glycolytic promoters. Electrophoretic mobility shift assay indicated that recombinant Tgr protein specifically binds to promoter regions containing a TGM. Tgr was released from the DNA when maltotriose was added, suggesting that this sugar is most likely the physiological effector. Our results strongly suggest that Tgr is a global transcriptional regulator that simultaneously controls, in response to sugar availability, both glycolytic and gluconeogenic metabolism in T. kodakaraensis via its direct binding to the TGM.

}, keywords = {Amino Acid, Amino Acid Motifs, Amino Acid Sequence, Escherichia coli, Genetic, Genome, Genotype, Gluconeogenesis, Glycolysis, Molecular Sequence Data, Multienzyme Complexes, NADH, NADPH Oxidoreductases, Oligonucleotide Array Sequence Analysis, Promoter Regions, Pyrococcus furiosus, Recombinant Proteins, Sequence Homology, Thermococcus, Transcription}, issn = {0021-9258}, doi = {10.1074/jbc.M703424200}, author = {Kanai, Tamotsu and Akerboom, Jasper and Takedomi, Shogo and van de Werken, Harmen J G and Blombach, Fabian and van der Oost, John and Murakami, Taira and Atomi, Haruyuki and Imanaka, Tadayuki} } @article {46628, title = {GSK-3/Shaggy regulates olfactory habituation in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, year = {2007}, month = {2007 Mar 13}, pages = {4653-7}, abstract = {

Habituation is a universal form of nonassociative learning that results in the devaluation of sensory inputs that have little information content. Although habituation is found throughout nature and has been studied in many organisms, the underlying molecular mechanisms remain poorly understood. We performed a forward genetic screen in Drosophila to search for mutations that modified habituation of an olfactory-mediated locomotor startle response, and we isolated a mutation in the glycogen synthase kinase-3 (GSK-3) homolog Shaggy. Decreases in Shaggy levels blunted habituation, whereas increases promoted habituation. Additionally, habituation acutely regulated Shaggy by an inhibitory phosphorylation mechanism, suggesting that a signal transduction pathway that regulates Shaggy is engaged during habituation. Although shaggy mutations also affected circadian rhythm period, this requirement was genetically separable from its role in habituation. Thus, shaggy functions in different neuronal circuits to regulate behavioral plasticity to an olfactory startle and circadian rhythmicity.

}, keywords = {Alleles, Animals, Behavior, Animal, Circadian Rhythm, Drosophila, Drosophila Proteins, Female, Glycogen Synthase Kinase 3, Habituation, Psychophysiologic, Male, Models, Genetic, Mutation, Phosphorylation, Signal Transduction, Smell}, issn = {0027-8424}, doi = {10.1073/pnas.0700493104}, author = {Wolf, Fred W and Eddison, Mark and Lee, Seonok and Cho, William and Heberlein, Ulrike} } @article {46630, title = {Guidelines on nicotine dose selection for in vivo research.}, journal = {Psychopharmacology (Berl)}, volume = {190}, year = {2007}, month = {2007 Feb}, pages = {269-319}, abstract = {

RATIONALE: This review provides insight for the judicious selection of nicotine dose ranges and routes of administration for in vivo studies. The literature is replete with reports in which a dosaging regimen chosen for a specific nicotine-mediated response was suboptimal for the species used. In many cases, such discrepancies could be attributed to the complex variables comprising species-specific in vivo responses to acute or chronic nicotine exposure.

OBJECTIVES: This review capitalizes on the authors{\textquoteright} collective decades of in vivo nicotine experimentation to clarify the issues and to identify the variables to be considered in choosing a dosaging regimen. Nicotine dose ranges tolerated by humans and their animal models provide guidelines for experiments intended to extrapolate to human tobacco exposure through cigarette smoking or nicotine replacement therapies. Just as important are the nicotine dosaging regimens used to provide a mechanistic framework for acquisition of drug-taking behavior, dependence, tolerance, or withdrawal in animal models.

RESULTS: Seven species are addressed: humans, nonhuman primates, rats, mice, Drosophila, Caenorhabditis elegans, and zebrafish. After an overview on nicotine metabolism, each section focuses on an individual species, addressing issues related to genetic background, age, acute vs chronic exposure, route of administration, and behavioral responses.

CONCLUSIONS: The selected examples of successful dosaging ranges are provided, while emphasizing the necessity of empirically determined dose-response relationships based on the precise parameters and conditions inherent to a specific hypothesis. This review provides a new, experimentally based compilation of species-specific dose selection for studies on the in vivo effects of nicotine.

}, keywords = {Animals, Behavioral Research, Dose-Response Relationship, Drug, Ganglionic Stimulants, Guidelines as Topic, Humans, Models, Biological, Nicotine, Species Specificity}, issn = {0033-3158}, doi = {10.1007/s00213-006-0441-0}, author = {Matta, Shannon G and Balfour, David J and Benowitz, Neal L and Boyd, R Thomas and Buccafusco, Jerry J and Caggiula, Anthony R and Craig, Caroline R and Collins, Allan C and Damaj, M Imad and Donny, Eric C and Gardiner, Phillip S and Grady, Sharon R and Heberlein, Ulrike and Leonard, Sherry S and Levin, Edward D and Lukas, Ronald J and Markou, Athina and Marks, Michael J and McCallum, Sarah E and Parameswaran, Neeraja and Perkins, Kenneth A and Picciotto, Marina R and Quik, Maryka and Rose, Jed E and Rothenfluh, Adrian and Schafer, William R and Stolerman, Ian P and Tyndale, Rachel F and Wehner, Jeanne M and Zirger, Jeffrey M} } @article {1188, title = {Genesis and wanderings: origins and migrations in asymmetrically replicating mitochondrial DNA.}, journal = {Cell Cycle}, volume = {5}, year = {2006}, month = {2006 May}, pages = {917-21}, abstract = {

Mammalian mitochondria maintain a small circular genome that encodes RNA and polypeptides that are essential for the generation of ATP through oxidative phosphorylation. The mechanism of replication of mammalian mitochondrial DNA (mtDNA) has recently been a topic of controversy. New evidence has led to a modified strand-displacement model that reconciles much of the current data. This revision stems from a new appreciation for alternative light-strand origins. We consider here some of the potential mechanisms for light-strand origin initiation. We also consider further the susceptibility of branch migration within replicating mtDNA molecules. The existence of alternative light-strand origins and a propensity for branch migration in replicating mtDNA molecules exposes a new array of possible configurations of mtDNA. The assortment and assignment of these forms is relevant to the interpretation of experimental data and may also yield insight into the molecular basis of replication errors.

}, keywords = {Animals, Atomic Force, DNA, DNA Replication, Electrophoresis, Evolution, Gel, Genetic, Microscopy, Mitochondrial, Models, Molecular, Two-Dimensional}, issn = {1551-4005}, author = {Brown, Timothy A and Clayton, David A} } @article {791, title = {Genetic mosaic with dual binary transcriptional systems in Drosophila.}, journal = {Nature Neuroscience}, volume = {9}, year = {2006}, month = {2006 May}, pages = {703-9}, abstract = {

MARCM (mosaic analysis with a repressible cell marker) involves specific labeling of GAL80-minus and GAL4-positive homozygous cells in otherwise heterozygous tissues. Here we demonstrate how the concurrent use of two independent binary transcriptional systems may facilitate complex MARCM studies in the Drosophila nervous system. By fusing LexA with the VP16 acidic activation domain (VP16) or the GAL4 activation domain (GAD), we obtained both GAL80-insensitive and GAL80-suppressible transcriptional factors. LexA::VP16 can mediate MARCM-independent binary transgene induction in mosaic organisms. The incorporation of LexA::GAD into MARCM, which we call dual-expression-control MARCM, permits the induction of distinct transgenes in different patterns among GAL80-minus cells in mosaic tissues. Lineage analysis with dual-expression-control MARCM suggested the presence of neuroglioblasts in the developing optic lobes but did not indicate the production of glia by postembryonic mushroom body neuronal precursors. In addition, dual-expression-control MARCM with a ubiquitous LexA::GAD driver revealed many unidentified cells in the GAL4-GH146-positive projection neuron lineages.

}, keywords = {Animals, Brain, Developmental, Drosophila, Drosophila Proteins, Gene Expression Regulation, Genetically Modified, Immunohistochemistry, Models, Molecular, Mosaicism, Neurons, Repressor Proteins, Transcription Factors, Transcriptional Activation}, issn = {1097-6256}, doi = {10.1038/nn1681}, author = {Lai, Sen-Lin and Lee, Tzumin} } @article {792, title = {Gradients of the Drosophila Chinmo BTB-zinc finger protein govern neuronal temporal identity.}, journal = {Cell}, volume = {127}, year = {2006}, month = {2006 Oct 20}, pages = {409-22}, abstract = {

Many neural progenitors, including Drosophila mushroom body (MB) and projection neuron (PN) neuroblasts, sequentially give rise to different subtypes of neurons throughout development. We identified a novel BTB-zinc finger protein, named Chinmo (Chronologically inappropriate morphogenesis), that governs neuronal temporal identity during postembryonic development of the Drosophila brain. In both MB and PN lineages, loss of Chinmo autonomously causes early-born neurons to adopt the fates of late-born neurons from the same lineages. Interestingly, primarily due to a posttranscriptional control, MB neurons born at early developmental stages contain more abundant Chinmo than their later-born siblings. Further, the temporal identity of MB progeny can be transformed toward earlier or later fates by reducing or increasing Chinmo levels, respectively. Taken together, we suggest that a temporal gradient of Chinmo (Chinmo(high) {\textendash}\> Chinmo(low)) helps specify distinct birth order-dependent cell fates in an extended neuronal lineage.

}, keywords = {5{\textquoteright} Untranslated Regions, Amino Acid Sequence, Animals, Brain, Cell Differentiation, Cell Lineage, Developmental, Drosophila, Drosophila Proteins, Gene Expression Regulation, Larva, Molecular Sequence Data, Morphogenesis, Mushroom Bodies, Mutation, Nerve Tissue Proteins, Neurons, Post-Translational, Protein Processing, Time Factors, Transgenes, Zinc Fingers}, issn = {0092-8674}, doi = {10.1016/j.cell.2006.08.045}, author = {Zhu, Sijun and Lin, Suewei and Kao, Chih-Fei and Awasaki, Takeshi and Chiang, Ann-Shyn and Lee, Tzumin} } @article {45759, title = {Genetic mapping of aphicarus -- a sex-linked locus controlling a wing polymorphism in the pea aphid (Acyrthosiphon pisum).}, journal = {Heredity (Edinb)}, volume = {94}, year = {2005}, month = {2005 Apr}, pages = {435-42}, abstract = {

We have initiated research to determine the genetic basis of a male wing polymorphism in the pea aphid Acyrthosiphon pisum (Hemiptera: Aphididae). Previous studies showed that this polymorphism is controlled by a single biallelic locus, which we name aphicarus (api), on the X chromosome. Our objectives were to confirm that api segregates as a polymorphism of a single gene on the X chromosome, and to obtain molecular markers flanking api that can be used as a starting point for high-resolution genetic and physical mapping of the target region, which will ultimately allow the cloning of api. We have established an F2 population segregating for api and have generated X-linked AFLP markers. The segregation pattern of api in the F2 population shows that the male wing polymorphism segregates as a polymorphism of a single gene, or set of closely linked genes on the X chromosome. Using a subset of 78 F2 males, we have constructed a linkage map of the chromosomal region encompassing api using seven AFLP markers. The map spans 74.1 cM and we have mapped api to an interval of 10 cM. In addition, we confirmed X linkage of our AFLP markers and api by using one X-linked marker developed in an earlier study. Our study presents the first mapping of a gene with known function in aphids, and the results indicate that target gene mapping in aphids is feasible.

}, keywords = {Animals, Aphids, Chromosome Mapping, Genetic Markers, Linkage Disequilibrium, Male, Polymorphism, Genetic, Quantitative Trait Loci, Random Amplified Polymorphic DNA Technique, Wing, X Chromosome}, issn = {0018-067X}, doi = {10.1038/sj.hdy.6800633}, author = {Braendle, C and Caillaud, M C and Stern, D L} } @article {45756, title = {Genetic variation for an aphid wing polyphenism is genetically linked to a naturally occurring wing polymorphism.}, journal = {Proc Biol Sci}, volume = {272}, year = {2005}, month = {2005 Mar 22}, pages = {657-64}, abstract = {

Many polyphenisms are examples of adaptive phenotypic plasticity where a single genotype produces distinct phenotypes in response to environmental cues. Such alternative phenotypes occur as winged and wingless parthenogenetic females in the pea aphid (Acyrthosiphon pisum). However, the proportion of winged females produced in response to a given environmental cue varies between clonal genotypes. Winged and wingless phenotypes also occur in males of the sexual generation. In contrast to parthenogenetic females, wing production in males is environmentally insensitive and controlled by the sex-linked, biallelic locus, aphicarus (api). Hence, environmental or genetic cues induce development of winged and wingless phenotypes at different stages of the pea aphid life cycle. We have tested whether allelic variation at the api locus explains genetic variation in the propensity to produce winged females. We assayed clones from an F2 cross that were heterozygous or homozygous for alternative api alleles for their propensity to produce winged offspring. We found that clones with different api genotypes differed in their propensity to produce winged offspring. The results indicate genetic linkage of factors controlling the female wing polyphenism and male wing polymorphism. This finding is consistent with the hypothesis that genotype by environment interaction at the api locus explains genetic variation in the environmentally cued wing polyphenism.

}, keywords = {Alleles, Analysis of Variance, Animals, Aphids, Crosses, Genetic, Crowding, Female, Food Deprivation, Genes, Insect, Genetic Linkage, Genetic Variation, Genotype, Male, Phenotype, Wing}, issn = {0962-8452}, doi = {10.1098/rspb.2004.2995}, author = {Braendle, Christian and Friebe, Ilvy and Caillaud, Marina C and Stern, David L} } @article {1250, title = {Geometric and functional organization of cortical circuits.}, journal = {Nature Neuroscience}, volume = {8}, year = {2005}, month = {2005 Jun}, pages = {782-90}, abstract = {

Can neuronal morphology predict functional synaptic circuits? In the rat barrel cortex, {\textquoteright}barrels{\textquoteright} and {\textquoteright}septa{\textquoteright} delineate an orderly matrix of cortical columns. Using quantitative laser scanning photostimulation we measured the strength of excitatory projections from layer 4 (L4) and L5A to L2/3 pyramidal cells in barrel- and septum-related columns. From morphological reconstructions of excitatory neurons we computed the geometric circuit predicted by axodendritic overlap. Within most individual projections, functional inputs were predicted by geometry and a single scale factor, the synaptic strength per potential synapse. This factor, however, varied between projections and, in one case, even within a projection, up to 20-fold. Relationships between geometric overlap and synaptic strength thus depend on the laminar and columnar locations of both the pre- and postsynaptic neurons, even for neurons of the same type. A large plasticity potential appears to be incorporated into these circuits, allowing for functional {\textquoteright}tuning{\textquoteright} with fixed axonal and dendritic arbor geometry.

}, keywords = {Animals, Axons, Brain Mapping, Cell Shape, Dendrites, Electric Stimulation, Excitatory Postsynaptic Potentials, Image Cytometry, Lasers, Lysine, Neural Pathways, Neuronal Plasticity, Organ Culture Techniques, Photic Stimulation, Pyramidal Cells, Rats, Somatosensory Cortex, Sprague-Dawley, Synapses, Synaptic Transmission, Ultraviolet Rays}, issn = {1097-6256}, doi = {10.1016/j.tins.2005.05.006}, author = {Shepherd, Gordon M G and Stepanyants, Armen and Bureau, Ingrid and Chklovskii, Dmitri and Svoboda, Karel} } @article {46631, title = {GPCR signaling is required for blood-brain barrier formation in drosophila.}, journal = {Cell}, volume = {123}, year = {2005}, month = {2005 Oct 7}, pages = {133-44}, abstract = {

The blood-brain barrier of Drosophila is established by surface glia, which ensheath the nerve cord and insulate it against the potassium-rich hemolymph by forming intercellular septate junctions. The mechanisms underlying the formation of this barrier remain obscure. Here, we show that the G protein-coupled receptor (GPCR) Moody, the G protein subunits G alpha i and G alpha o, and the regulator of G protein signaling Loco are required in the surface glia to achieve effective insulation. Our data suggest that the four proteins act in a complex common pathway. At the cellular level, the components function by regulating the cortical actin and thereby stabilizing the extended morphology of the surface glia, which in turn is necessary for the formation of septate junctions of sufficient length to achieve proper sealing of the nerve cord. Our study demonstrates the importance of morphogenetic regulation in blood-brain barrier development and places GPCR signaling at its core.

}, keywords = {Actins, Alternative Splicing, Animals, Blood-Brain Barrier, Brain, Drosophila melanogaster, Drosophila Proteins, Endothelium, Vascular, GTP-Binding Protein alpha Subunits, Gi-Go, Microscopy, Electron, Transmission, Nerve Tissue Proteins, Neuroglia, Receptors, G-Protein-Coupled, Signal Transduction, Tight Junctions}, issn = {0092-8674}, doi = {10.1016/j.cell.2005.08.037}, author = {Schwabe, Tina and Bainton, Roland J and Fetter, Richard D and Heberlein, Ulrike and Gaul, Ulrike} } @article {45801, title = {Gene Expression in Acyrthosiphon Pisum (Hemiptera: Aphididae)}, journal = {National Center for Biotechnology Information (NCBI)}, year = {2004}, month = {03/2004}, abstract = {

Examination of the genetic differences between aphids that can transmit citrus tristeza virus, CTV, and those which cannot, may lead to a greater understanding of the virus-aphid interactions necessitating virus acquisition and transmission. Since a cDNA library had been completed the previous year for the brown citrus aphid, a vector of CTV, a second aphid cDNA library was made to a non-CTV aphid vector, the pea aphid, Acyrthosiphon pisum. Comparisons between these two genetic datasets will provide a better understanding of the dynamics of aphid feeding, digestion, development, and may elucidate elements related to virus interactions that were previously unknown. Identification of the numerous proteins actively involved in feeding and digestion from aphids will provide specific targets for the development of new methods of control aimed at disrupting aphid feeding and ultimately reducing the acquisition and transmission of plant viruses which cause disease.

}, url = {http://www.ars.usda.gov/research/publications/publications.htm?SEQ_NO_115=168710}, author = {WB Hunter and PM Dang and D Stern} } @article {2380, title = {Genetic specification of axonal arbors: atonal regulates robo3 to position terminal branches in the Drosophila nervous system.}, journal = {Neuron}, volume = {37}, year = {2003}, month = {2003 Jan 9}, pages = {41-51}, abstract = {

Drosophila sensory neurons form distinctive terminal branch patterns in the developing neuropile of the embryonic central nervous system. In this paper we make a genetic analysis of factors regulating arbor position. We show that mediolateral position is determined in a binary fashion by expression (chordotonal neurons) or nonexpression (multidendritic neurons) of the Robo3 receptor for the midline repellent Slit. Robo3 expression is one of a suite of chordotonal neuron properties that depend on expression of the proneural gene atonal. Different features of terminal branches are separately regulated: an arbor can be shifted mediolaterally without affecting its dorsoventral location, and the distinctive remodeling of one arbor continues as normal despite this arbor shifting to an abnormal position in the neuropile.

}, keywords = {Afferent, Animals, Axons, Basic Helix-Loop-Helix Transcription Factors, Cell Communication, Cell Differentiation, Developmental, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Embryo, Female, Functional Laterality, Gene Expression Regulation, Growth Cones, Immunologic, Larva, Male, Membrane Proteins, Mutation, Nerve Tissue Proteins, Nervous System, Nervous System Malformations, Neuronal Plasticity, Neurons, Nonmammalian, Presynaptic Terminals, Receptors}, issn = {0896-6273}, author = {Zlatic, Marta and Landgraf, Matthias and Bate, Michael} } @article {1143, title = {A genomic analysis of gene expresson during the Drosophila life cycle.}, journal = {Science}, year = {2002}, month = {2002}, pages = {2270-75}, author = {Baker, B.S. and Arbeitman, M. and Furlong, E. and Imam, F. and Johnson, E. and Null, B.} } @article {1259, title = {Geometry and structural plasticity of synaptic connectivity.}, journal = {Neuron}, volume = {34}, year = {2002}, month = {2002 Apr 11}, pages = {275-88}, abstract = {

Changes in synaptic connectivity patterns through the formation and elimination of dendritic spines may contribute to structural plasticity in the brain. We characterize this contribution quantitatively by estimating the number of different synaptic connectivity patterns attainable without major arbor remodeling. This number depends on the ratio of the synapses on a dendrite to the axons that pass within a spine length of that dendrite. We call this ratio the filling fraction and calculate it from geometrical analysis and anatomical data. The filling fraction is 0.26 in mouse neocortex, 0.22-0.34 in rat hippocampus. In the macaque visual cortex, the filling fraction increases by a factor of 1.6-1.8 from area V1 to areas V2, V4, and 7a. Since the filling fraction is much smaller than 1, spine remodeling can make a large contribution to structural plasticity.

}, keywords = {Animals, Macaca fascicularis, Male, Models, Neural Pathways, Neurological, Neuronal Plasticity, Synapses}, issn = {0896-6273}, doi = {10.1016/j.tins.2005.05.006}, author = {Stepanyants, Armen and Hof, Patrick R and Chklovskii, Dmitri B} } @article {1988, title = {Glutamate-mediated extrasynaptic inhibition: direct coupling of NMDA receptors to Ca(2+)-activated K+ channels.}, journal = {Neuron}, volume = {31}, year = {2001}, month = {2001 Sep 27}, pages = {1027-34}, abstract = {

NMDA receptors (NMDARs) typically contribute to excitatory synaptic transmission in the CNS. While Ca(2+) influx through NMDARs plays a critical role in synaptic plasticity, direct actions of NMDAR-mediated Ca(2+) influx on neuronal excitability have not been well established. Here we show that Ca(2+) influx through NMDARs is directly coupled to activation of BK-type Ca(2+)-activated K+ channels in outside-out membrane patches from rat olfactory bulb granule cells. Repetitive stimulation of glutamatergic synapses in olfactory bulb slices evokes a slow inhibitory postsynaptic current (IPSC) in granule cells that requires both NMDARs and BK channels. The slow IPSC is enhanced by glutamate uptake blockers, suggesting that extrasynaptic NMDARs underlie the response. These findings reveal a novel inhibitory action of extrasynaptic NMDARs in the brain.

}, keywords = {Animals, Calcium, Calcium Channel Blockers, Calcium Channels, Calcium-Activated, Evoked Potentials, Excitatory Postsynaptic Potentials, Glutamic Acid, Ion Channel Gating, Ion Transport, Large-Conductance Calcium-Activated Potassium Channels, Macromolecular Substances, Membrane Potentials, Models, N-Methyl-D-Aspartate, Nerve Tissue Proteins, Neurological, Neuronal Plasticity, Nicardipine, Olfactory Bulb, Olfactory Receptor Neurons, omega-Conotoxin GVIA, omega-Conotoxins, Patch-Clamp Techniques, Peptides, Potassium, Potassium Channels, Rats, Receptors, Smell, Sprague-Dawley}, issn = {0896-6273}, author = {Isaacson, J S and Murphy, G J} } @article {45952, title = {Galectin-3 is associated with the plasma membrane of lens fiber cells.}, journal = {Investigative Ophthalmology \& Visual Science}, volume = {41}, year = {2000}, month = {2000 Jan}, pages = {199-203}, abstract = {

PURPOSE: To discover proteins that have the potential to contribute to the tight packing of fiber cells in the lens.

METHODS: Crude fiber cell membranes were isolated from ovine lens cortex. Proteins were separated by two-dimensional gel electrophoresis, and selected protein spots identified by micro-sequencing. The identification of galectin-3 was confirmed by immunoblotting with a specific antibody. The association of galectin-3 with the fiber cell plasma membrane was investigated using immunofluorescence microscopy, solubilization trials with selected reagents, and immunoprecipitation to identify candidate ligands.

RESULTS: A cluster of three protein spots with an apparent molecular weight of 31,000 and isoelectric points ranging between 7 and 8.5 were resolved and identified as galectin-3. This protein was associated peripherally with the fiber cell plasma membrane and interacted with MP20, an abundant intrinsic membrane protein that had been identified previously as a component of membrane junctions between fiber cells.

CONCLUSIONS: The detection of galectin-3 in the lens is a novel result and adds to the growing list of lens proteins with adhesive properties. Its location at the fiber cell membrane and its association with the junction-forming MP20 is consistent with a potential role in the development or maintenance of the tightly packed lens tissue architecture.

}, keywords = {Amino Acid Sequence, Animals, Antigens, Differentiation, Cell Membrane, Chromatography, High Pressure Liquid, Electrophoresis, Gel, Two-Dimensional, Eye Proteins, Galectin 3, Immunoblotting, Lens Cortex, Crystalline, Ligands, Membrane Glycoproteins, Microscopy, Fluorescence, Molecular Sequence Data, Rabbits, Sequence Homology, Amino Acid, Sheep}, issn = {0146-0404}, author = {Gonen, T and Donaldson, P and Kistler, J} } @article {46643, title = {Genetic control of acute ethanol-induced behaviors in Drosophila.}, journal = {Alcoholism, Clinical and Experimental Research}, volume = {24}, year = {2000}, month = {2000 Aug}, pages = {1127-36}, abstract = {

BACKGROUND: In most organisms in which acute ethanol exposure has been studied, it leads to similar changes in behavior. Generally, low ethanol doses activate the central nervous system, whereas high doses are sedative. Sensitivity to the acute intoxicating effects of ethanol is in part under genetic control in rodents and humans, and reduced sensitivity in humans predicts the development of alcoholism (Crabbe et al., 1994; Schuckit, 1994). We have established Drosophila melanogaster as a model organism to study the mechanisms that regulate acute sensitivity to ethanol.

METHODS: We measured the effects of ethanol vapor on Drosophila locomotor behaviors by using three different assays. Horizontal locomotion was quantified in a locomotor chamber, turning behavior was assayed in narrow tubes, and ethanol-induced loss of postural control was measured in an inebriometer. Mutants with altered sensitivity to the acute effects of ethanol were generated by treatment with ethyl methane sulfonate and isolated by selection in the inebriometer. We ascertained the effects of these mutations on ethanol pharmacokinetics by measuring ethanol levels in extracts of flies at various times during and after ethanol exposure.

RESULTS: Among nearly 30,000 potentially mutant flies tested, we isolated 19 mutant strains with reduced and 4 strains with increased sensitivity to the acute effects of ethanol as measured in the inebriometer. Of these mutants, four showed changes in ethanol absorption. Two mutants, named barfly and tipsy to reflect their reduced and increased ethanol sensitivity in the inebriometer, respectively, were analyzed for locomotor behaviors. Both mutants exhibited ethanol-induced hyperactivity that was indistinguishable from wild type. However, barfly and tipsy displayed reduced and increased sensitivity to the sedative effects of ethanol, respectively. Finally, both mutants showed an increased rate of ethanol-induced turning behavior.

CONCLUSIONS: The effects of acute ethanol exposure on Drosophila locomotor behaviors are remarkably similar to those described for mammals. The analysis of mutants with altered sensitivity to ethanol revealed that the genetic pathways which regulate these responses are complex and that single genes can affect hyperactivity, turning, and sedation independently.

}, keywords = {Absorption, Animals, Behavior, Animal, Drosophila melanogaster, Drug Resistance, Ethanol, Kinetics, Motor Activity, Mutation}, issn = {0145-6008}, author = {Singh, C M and Heberlein, U} } @article {957, title = {The genome sequence of Drosophila melanogaster.}, journal = {Science}, volume = {287}, year = {2000}, month = {2000 Mar 24}, pages = {2185-95}, abstract = {

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

}, keywords = {Animals, Biological Transport, Chromatin, Cloning, Computational Biology, Contig Mapping, Cytochrome P-450 Enzyme System, DNA, DNA Repair, DNA Replication, Drosophila melanogaster, Euchromatin, Gene Library, Genes, Genetic, Genome, Heterochromatin, Insect, Insect Proteins, Molecular, Nuclear Proteins, Protein Biosynthesis, Sequence Analysis, Transcription}, issn = {0036-8075}, doi = {10.1186/gb-2007-8-7-r145}, author = {Adams, M D and Celniker, S E and Holt, R A and Evans, C A and Gocayne, J D and Amanatides, P G and Scherer, S E and Li, P W and Hoskins, R A and Galle, R F and George, R A and Lewis, S E and Richards, S and Ashburner, M and Henderson, S N and Sutton, G G and Wortman, J R and Yandell, M D and Zhang, Q and Chen, L X and Brandon, R C and Rogers, Y H and Blazej, R G and Champe, M and Pfeiffer, B D and Wan, K H and Doyle, C and Baxter, E G and Helt, G and Nelson, C R and Gabor, G L and Abril, J F and Agbayani, A and An, H J and Andrews-Pfannkoch, C and Baldwin, D and Ballew, R M and Basu, A and Baxendale, J and Bayraktaroglu, L and Beasley, E M and Beeson, K Y and Benos, P V and Berman, B P and Bhandari, D and Bolshakov, S and Borkova, D and Botchan, M R and Bouck, J and Brokstein, P and Brottier, P and Burtis, K C and Busam, D A and Butler, H and Cadieu, E and Center, A and Chandra, I and Cherry, J M and Cawley, S and Dahlke, C and Davenport, L B and Davies, P and de Pablos, B and Delcher, A and Deng, Z and Mays, A D and Dew, I and Dietz, S M and Dodson, K and Doup, L E and Downes, M and Dugan-Rocha, S and Dunkov, B C and Dunn, P and Durbin, K J and Evangelista, C C and Ferraz, C and Ferriera, S and Fleischmann, W and Fosler, C and Gabrielian, A E and Garg, N S and Gelbart, W M and Glasser, K and Glodek, A and Gong, F and Gorrell, J H and Gu, Z and Guan, P and Harris, M and Harris, N L and Harvey, D and Heiman, T J and Hernandez, J R and Houck, J and Hostin, D and Houston, K A and Howland, T J and Wei, M H and Ibegwam, C and Jalali, M and Kalush, F and Karpen, G H and Ke, Z and Kennison, J A and Ketchum, K A and Kimmel, B E and Kodira, C D and Kraft, C and Kravitz, S and Kulp, D and Lai, Z and Lasko, P and Lei, Y and Levitsky, A A and Li, J and Li, Z and Liang, Y and Lin, X and Liu, X and Mattei, B and McIntosh, T C and McLeod, M P and McPherson, D and Merkulov, G and Milshina, N V and Mobarry, C and Morris, J and Moshrefi, A and Mount, S M and Moy, M and Murphy, B and Murphy, L and Muzny, D M and Nelson, D L and Nelson, D R and Nelson, K A and Nixon, K and Nusskern, D R and Pacleb, J M and Palazzolo, M and Pittman, G S and Pan, S and Pollard, J and Puri, V and Reese, M G and Reinert, K and Remington, K and Saunders, R D and Scheeler, F and Shen, H and Shue, B C and Sid{\'e}n-Kiamos, I and Simpson, M and Skupski, M P and Smith, T and Spier, E and Spradling, A C and Stapleton, M and Strong, R and Sun, E and Svirskas, R and Tector, C and Turner, R and Venter, E and Wang, A H and Wang, X and Wang, Z Y and Wassarman, D A and Weinstock, G M and Weissenbach, J and Williams, S M and Williams, S M and Worley, K C and Wu, D and Yang, S and Yao, Q A and Ye, J and Yeh, R F and Zaveri, J S and Zhan, M and Zhang, G and Zhao, Q and Zheng, L and Zheng, X H and Zhong, F N and Zhong, W and Zhou, X and Zhu, S and Zhu, X and Smith, H O and Gibbs, R A and Myers, E W and Rubin, G M and Venter, J C} } @article {1213, title = {GFP tagging of budding yeast chromosomes reveals that protein-protein interactions can mediate sister chromatid cohesion.}, journal = {Current Biology}, volume = {6}, year = {1996}, month = {1996 Dec 1}, pages = {1599-608}, abstract = {

Precise control of sister chromatid separation is essential for the accurate transmission of genetic information. Sister chromatids must remain linked to each other from the time of DNA replication until the onset of chromosome segregation, when the linkage must be promptly dissolved. Recent studies suggest that the machinery that is responsible for the destruction of mitotic cyclins also degrades proteins that play a role in maintaining sister chromatid linkage, and that this machinery is regulated by the spindle-assembly checkpoint. Studies on these problems in budding yeast are hampered by the inability to resolve its chromosomes by light or electron microscopy.

}, keywords = {Bacterial Proteins, Chromatids, Chromosomes, Escherichia coli Proteins, Fungal, Gene Expression, Green Fluorescent Proteins, Lac Repressors, Luminescent Proteins, Proteins, Recombinant Fusion Proteins, Repressor Proteins, Signal Transduction, Yeasts}, issn = {0960-9822}, author = {Straight, A F and Belmont, A S and Robinett, C C and Murray, A W} } @article {46654, title = {Growth and differentiation in the Drosophila eye coordinated by hedgehog.}, journal = {Nature}, volume = {373}, year = {1995}, month = {1995 Feb 23}, pages = {709-11}, abstract = {

Differentiation of the Drosophila retina is asynchronous: it starts at the posterior margin of the eye imaginal disc and progresses anteriorly over two days. During this time the disc continues to grow, increasing in size by approximately eightfold. An indentation in the epithelium, the morphogenetic furrow, marks the front edge of the differentiation wave. Anterior progression of the furrow is thought to be driven by signals emanating from differentiating photoreceptor cells in the posterior eye disc. A good candidate for such a signal is the product of the hedgehog (hh) gene; it is expressed, and presumably secreted, by differentiating photoreceptors and its function is required for continued furrow movement. Here we show that ectopic expression of hedgehog sets in motion ectopic furrows in the anterior eye disc. In addition to changes in cell shape, these ectopic furrows are associated with a tightly orchestrated series of events, including proliferation, cell cycle synchronization and pattern formation, that parallel normal furrow progression. We propose that the morphogenetic furrow coincides with a transient boundary that coordinates growth and differentiation of the eye disc, and that hedgehog is necessary and sufficient to propagate this boundary across the epithelium.

}, keywords = {Animals, Basic Helix-Loop-Helix Transcription Factors, Cell Cycle, Cell Cycle Proteins, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Embryonic Induction, Eye, Hedgehog Proteins, Helix-Loop-Helix Motifs, Insect Hormones, Insect Proteins, Nerve Tissue Proteins, Phosphoprotein Phosphatases, Protein Tyrosine Phosphatases, Proteins, Repressor Proteins, Signal Transduction, Transcription Factors}, issn = {0028-0836}, doi = {10.1038/373709a0}, author = {Heberlein, U and Singh, C M and Luk, A Y and Donohoe, T J} } @article {972, title = {The glass gene encodes a zinc-finger protein required by Drosophila photoreceptor cells.}, journal = {Nature}, volume = {340}, year = {1989}, month = {1989 Aug 17}, pages = {531-6}, abstract = {

Null mutations of glass specifically remove photoreceptor cells, leaving other cell types intact. We have isolated the glass gene and have shown that its transcript encodes a putative protein of 604 amino acids with five zinc-fingers. The glass product may be a transcription factor required for the development of a single neuronal cell type.

}, keywords = {Animals, Base Sequence, DNA, Drosophila, Gene Expression Regulation, Molecular Sequence Data, Mutation, Photoreceptor Cells}, issn = {0028-0836}, doi = {10.1186/gb-2007-8-7-r145}, author = {Moses, K and Ellis, M C and Rubin, G M} } @article {980, title = {Genetic transformation of Drosophila with transposable element vectors.}, journal = {Science}, volume = {218}, year = {1982}, month = {1982 Oct 22}, pages = {348-53}, abstract = {

Exogenous DNA sequences were introduced into the Drosophila germ line. A rosy transposon (ry1), constructed by inserting a chromosomal DNA fragment containing the wild-type rosy gene into a P transposable element, transformed germ line cells in 20 to 50 percent of the injected rosy mutant embryos. Transformants contained one or two copies of chromosomally integrated, intact ry1 that were stably inherited in subsequent generations. These transformed flies had wild-type eye color indicating that the visible genetic defect in the host strain could be fully and permanently corrected by the transferred gene. To demonstrate the generality of this approach, a DNA segment that does not confer a recognizable phenotype on recipients was also transferred into germ line chromosomes.

}, keywords = {Animals, Chromosome Mapping, DNA Transposable Elements, Drosophila, Genes, Genetic, Genetic Engineering, Mutation, Nucleic Acid Hybridization, Plasmids, Transformation, Xanthine Dehydrogenase}, issn = {0036-8075}, doi = {10.1186/gb-2007-8-7-r145}, author = {Rubin, G M and Spradling, A C} }