Difference between revisions of "FlyBase:Papers with technical advances"

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==Technical Advances==
 
==Technical Advances==
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===2022===
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==== Nov 2022====
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! ''Author description of technical advance''!!''Title''!!''Journal''!!''PubMed ID''!! ''FBrf number''
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| Endogenously tagged RNA polymerase II subunits, including mCherry-Rpb1 and EGFP-Rpb3.||Coordinating transcription and replication to mitigate their conflicts in early Drosophila embryos.||Cell Rep.||[https://pubmed.ncbi.nlm.nih.gov/36261005  36261005 ]||[https://flybase.org/reports/FBrf0254801 FBrf0254801]
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| AO-SOLEIL mitigates deep tissue-induced deteriorations and was applied on dSTORM samples in adult Drosophila brains. A 2x improvement in the estimated axial localization precision with respect to widefield without aberration correction was observed.||Adaptive optics in single objective inclined light sheet microscopy enables three-dimensional localization microscopy in adult Drosophila brains.||Front. Neurosci.||[https://pubmed.ncbi.nlm.nih.gov/36278016  36278016 ]||[https://flybase.org/reports/FBrf0254788 FBrf0254788]
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| (Z)-4-undecenal is the female pheromone of cosmopolitan D. melanogaster, an oxidation product of the aphrodisiac hydrocarbon (Z,Z)-7,11-heptacosadiene. Females of the Zimbabwe strain release also (Z)-4-nonenal, since they produce another hydrocarbon, (Z,Z)-5,9-heptacosadiene.||The human odorant receptor OR10A6 is tuned to the pheromone of the commensal fruit fly Drosophila melanogaster.||iScience||[https://pubmed.ncbi.nlm.nih.gov/36300000  36300000 ]||[https://flybase.org/reports/FBrf0254861 FBrf0254861]
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| Population recordings of descending neurons during behavior.||Descending neuron population dynamics during odor-evoked and spontaneous limb-dependent behaviors.||eLife||[https://pubmed.ncbi.nlm.nih.gov/36286408  36286408 ]||[https://flybase.org/reports/FBrf0254871 FBrf0254871]
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| Transgenes encoding HaloTag-based reporters for sparse labeling.||HaloTag-based reporters for sparse labeling and cell tracking.||Fly||[https://pubmed.ncbi.nlm.nih.gov/36323649  36323649 ]||[https://flybase.org/reports/FBrf0254955 FBrf0254955]
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| Expression of different heat shock proteins during defined stages progression of epithelial malignant tumors of different genetic backgrounds.||Delayed discovery of Hsp60 and subsequent characterization of moonlighting functions of multiple Hsp60 genes in Drosophila: a personal historical perspective.||J. Genet.||[https://pubmed.ncbi.nlm.nih.gov/36330787  36330787 ]||[https://flybase.org/reports/FBrf0254951 FBrf0254951]
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| We performed FRET data analysis using Matlab to visualize ATP concentration in living wing disc explants, then described the kinetics of FRET efficiency drop upon use of metabolic drugs targeting glycolysis and/or OxPhos in wt discs or discs with up/down-regulated Hh signaling.||Hedgehog signaling can enhance glycolytic ATP production in the Drosophila wing disc.||EMBO Rep.||[https://pubmed.ncbi.nlm.nih.gov/36134875  36134875 ]||[https://flybase.org/reports/FBrf0254957 FBrf0254957]
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| Protocol for using bioluminescent bacteria to track infection.||Longitudinal monitoring of individual infection progression in Drosophila melanogaster.||iScience||[https://pubmed.ncbi.nlm.nih.gov/36345341  36345341 ]||[https://flybase.org/reports/FBrf0254928 FBrf0254928]
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| In this paper, we made a high-quality and annotated sequencing of Drosophila nebulosa. In addition, we employed CRISPR/Cas9 to disrupt the White gene. This gene was found to be necessary for D. nebulosa mating. ||Nebulous without white: annotated long-read genome assembly and CRISPR/Cas9 genome engineering in Drosophila nebulosa.||G3 (Bethesda)||[https://pubmed.ncbi.nlm.nih.gov/36063049  36063049 ]||[https://flybase.org/reports/FBrf0254926 FBrf0254926]
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| New in silico model for cell-cell interaction for Hedgehog signaling. ||Predictive model for cytoneme guidance in Hedgehog signaling based on Ihog- Glypicans interaction.||Nat. Commun.||[https://pubmed.ncbi.nlm.nih.gov/36163184  36163184 ]||[https://flybase.org/reports/FBrf0254595 FBrf0254595]
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| RT&Tag uses antibodies to tether tagmentation reagents in situ in the nucleus for profiling of localized RNAs. The method has been used for profiling RNAs associated with silenced or active chromatin, or with RNA modifications. ||Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation.||Nat. Methods||[https://pubmed.ncbi.nlm.nih.gov/36192462  36192462 ]||[https://flybase.org/reports/FBrf0254922 FBrf0254922]
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| This paper describes a bioinformatics workflow designed to map insertions of natural transposons in genomes of interest with Genome ARTIST_v2, a software developed by our research team.||Genome ARTIST_v2-An Autonomous Bioinformatics Tool for Annotation of Natural Transposons in Sequenced Genomes.||Int. J. Mol. Sci.||[https://pubmed.ncbi.nlm.nih.gov/36293549  36293549 ]||[https://flybase.org/reports/FBrf0254901 FBrf0254901]
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| We demonstrate stimulated Raman scattering spectro-microscopy driven by a multiple-plate continuum, enable spectroscopic interrogation across the entire Drosophila brain and electronic pre-resonance detection of a fluorescent dye.||Towards stimulated Raman scattering spectro-microscopy across the entire Raman active region using a multiple-plate continuum.||Opt. Express||[https://pubmed.ncbi.nlm.nih.gov/36258449  36258449 ]||[https://flybase.org/reports/FBrf0254804 FBrf0254804]
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| Using 3D electron and light microscopy, we found the mitochondrial network distribution of Drosophila melanogaster strikingly similar to mouse cardiac and oxidative muscles. Proteomic analyses on indirect flight, jump, and leg muscles.||Identification of evolutionarily conserved regulators of muscle mitochondrial network organization.||Nat. Commun.||[https://pubmed.ncbi.nlm.nih.gov/36333356  36333356 ]||[https://flybase.org/reports/FBrf0254964 FBrf0254964]
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| Optogenetic perturbation of aPKC in vivo, based on LARIAT system and GFP-aPKC knock-in line.||aPKC regulates apical constriction to prevent tissue rupture in the Drosophila follicular epithelium.||Curr. Biol.||[https://pubmed.ncbi.nlm.nih.gov/36113470  36113470 ]||[https://flybase.org/reports/FBrf0254903 FBrf0254903]
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| Express Drosophila striated muscle myosin using Sf9/baculovirus system. ||Insect Sf9 cells are suitable for functional expression of insect, but not vertebrate, striated muscle myosin.||Biochem. Biophys. Res. Commun.||[https://pubmed.ncbi.nlm.nih.gov/36308905  36308905 ]||[https://flybase.org/reports/FBrf0255002 FBrf0255002]
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| A new stable 8X tissue expansion method and computational tools to reconstruct neural circuit structure in Drosophila using expansion microscopy. All tools are available on GitHub (https://github.com/JaneliaSciComp/exllsm-circuit-reconstruction). ||Rapid reconstruction of neural circuits using tissue expansion and light sheet microscopy.||eLife||[https://pubmed.ncbi.nlm.nih.gov/36286237  36286237 ]||[https://flybase.org/reports/FBrf0255018 FBrf0255018]
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| New model to analyse significant interactions from Hi-C and micro-C data.||ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C data.||Bioinformatics||[https://pubmed.ncbi.nlm.nih.gov/35678507  35678507 ]||[https://flybase.org/reports/FBrf0255007 FBrf0255007]
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| A microfluidic microinjection technique and heartbeat quantification software were introduced which may help to perform cardiac toxicity studies. ||An in-vivo microfluidic assay reveals cardiac toxicity of heavy metals and the protective effect of metal responsive transcription factor (MTF-1) in Drosophila model.||3 Biotech||[https://pubmed.ncbi.nlm.nih.gov/36275358  36275358 ]||[https://flybase.org/reports/FBrf0254790 FBrf0254790]
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|}
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==== Oct 2022====
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{| class="wikitable"
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! ''Author description of technical advance''!!''Title''!!''Journal''!!''PubMed ID''!! ''FBrf number''
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| The paper describes a new muscle contraction model using Drosophila larvae and optogenetics. ||Modeling exercise using optogenetically contractible Drosophila larvae.||BMC Genomics||[https://pubmed.ncbi.nlm.nih.gov/36042416  36042416 ]||[https://flybase.org/reports/FBrf0254389 FBrf0254389]
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| Detailed description of tools for measuring cold tolerance under fictive cold stimuli via programmed optogenetic rearing. ||Protocols for measuring cold-evoked neural activity and cold tolerance in Drosophila larvae following fictive cold acclimation.||STAR Protoc||[https://pubmed.ncbi.nlm.nih.gov/35776643  35776643 ]||[https://flybase.org/reports/FBrf0254520 FBrf0254520]
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| LexAop transgenic lines and combining LexA and Gal4 together to study organ communication.||Renal NF-κB activation impairs uric acid homeostasis to promote tumor-associated mortality independent of wasting.||Immunity||[https://pubmed.ncbi.nlm.nih.gov/36029766  36029766 ]||[https://flybase.org/reports/FBrf0254493 FBrf0254493]
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| An improved method of conducting genome-wide mapping of chromatin protein binding sites termed nanoCut&Run.||The nanoCUT&RUN technique visualizes telomeric chromatin in Drosophila.||PLoS Genet.||[https://pubmed.ncbi.nlm.nih.gov/36048878  36048878 ]||[https://flybase.org/reports/FBrf0254524 FBrf0254524]
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| This paper identified variant PRC1 and PRC2.2 complexes in Drosophila using the BioTAP-XL technique. The previously unrecognized conservation of fly and mammalian PcG complexes provides a resource for improved understanding of epigenetic gene regulation in multicellular organisms.||Variant Polycomb complexes in Drosophila consistent with ancient functional diversity.||Sci. Adv.||[https://pubmed.ncbi.nlm.nih.gov/36070387  36070387 ]||[https://flybase.org/reports/FBrf0254426 FBrf0254426]
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| This paper describes a new light-gated expression tool LOV-LexA, in which the transcription factor LexA is shuttled into the nucleus to drive expression of LexAop sequences in the presence of blue light (405nm wavelength) but remains in the cytoplasm in the dark. ||Spatial and temporal control of expression with light-gated LOV-LexA.||G3 (Bethesda)||[https://pubmed.ncbi.nlm.nih.gov/35876796  35876796 ]||[https://flybase.org/reports/FBrf0254643 FBrf0254643]
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| New reagent: iRFP-tagged His2Av.||Near-infrared nuclear markers for Drosophila imaging.||MicroPubl Biol||[https://pubmed.ncbi.nlm.nih.gov/36212517  36212517 ]||[https://flybase.org/reports/FBrf0254678 FBrf0254678]
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| Allele dGao[47dsRed] is a platform for RMCE.||Restoration of the GTPase activity and cellular interactions of Gαo mutants by Zn2+ in GNAO1 encephalopathy models.||Sci. Adv.||[https://pubmed.ncbi.nlm.nih.gov/36206333  36206333 ]||[https://flybase.org/reports/FBrf0254662 FBrf0254662]
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| We present tauLUM, a Drosophila model that leverages split- luciferase technology to assay tau multimerization in vivo. TauLUM is a powerful discovery platform for identifying genetic regulators and drugs targeting tau multimerization.||TauLUM, an in vivo Drosophila sensor of tau multimerization, identifies neuroprotective interventions in tauopathy.||Cell Rep Methods||[https://pubmed.ncbi.nlm.nih.gov/36160048  36160048 ]||[https://flybase.org/reports/FBrf0254597 FBrf0254597]
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| This is an open access database for chromosome number and chromosome shape for Drosophila species and other dipterans.||Diptera and Drosophila Karyotype Databases: A Useful Dataset to Guide Evolutionary and Genomic Studies.||Front Ecol Evol||[https://pubmed.ncbi.nlm.nih.gov/36238425  36238425 ]||[https://flybase.org/reports/FBrf0254736 FBrf0254736]
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==== Sep 2022====
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{| class="wikitable"
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! ''Author description of technical advance''!!''Title''!!''Journal''!!''PubMed ID''!! ''FBrf number''
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| We used shotgun lipidomics and mass-spectrometry to analyze the impacts of vitamin A deficiency on the lipidome and the proteome of the Drosophila eye.||Vitamin A Deficiency Alters the Phototransduction Machinery and Distinct Non-Vision-Specific Pathways in the Drosophila Eye Proteome.||Biomolecules||[https://pubmed.ncbi.nlm.nih.gov/36008977  36008977 ]||[https://flybase.org/reports/FBrf0254376 FBrf0254376]
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| Multichannel magnetothermal activation of heat sensors using iron oxide nanoparticles.||Subsecond multichannel magnetic control of select neural circuits in freely moving flies.||Nat. Mater.||[https://pubmed.ncbi.nlm.nih.gov/35761060  35761060 ]||[https://flybase.org/reports/FBrf0254201 FBrf0254201]
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| Botulinum neurotoxin engineered for Gal4-mediated expression. When expressed in neurons, silences both evoked and spontaneous release. ||Botulinum neurotoxin accurately separates tonic vs. phasic transmission and reveals heterosynaptic plasticity rules in Drosophila.||eLife||[https://pubmed.ncbi.nlm.nih.gov/35993544  35993544 ]||[https://flybase.org/reports/FBrf0254399 FBrf0254399]
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| High resolution imaging of individual actin filaments in medioapical arrays in amnioserosa cells using grazing incidence, structured illumination.||Superresolution microscopy reveals actomyosin dynamics in medioapical arrays.||Mol. Biol. Cell||[https://pubmed.ncbi.nlm.nih.gov/35544300  35544300 ]||[https://flybase.org/reports/FBrf0254444 FBrf0254444]
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| Hypoxia protocol.||Standardized hypoxia-reoxygenation protocol to assess posthypoxic neurobehavioral impairments and molecular mechanisms in Drosophila melanogaster.||STAR Protoc||[https://pubmed.ncbi.nlm.nih.gov/36035795  36035795 ]||[https://flybase.org/reports/FBrf0254331 FBrf0254331]
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| Tools for effective control over the expression levels of transgenes are largely limited. We report a new series pUASTattB-based plasmids. These plasmids preserve the features of pUASTattB but contain a varying number of UAS sites. ||Generation and validation of pX-UASTattB for dose-dependent misexpression studies in Drosophila.||MicroPubl Biol||[https://pubmed.ncbi.nlm.nih.gov/36039330  36039330 ]||[https://flybase.org/reports/FBrf0254375 FBrf0254375]
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| Our study used a novel Rapamycin analog (Rapa* - 3Z) which specifically inhibits dTOR in presence of FKBP12-V55G mutant.||Tissue-restricted inhibition of mTOR using chemical genetics.||Proc. Natl. Acad. Sci. U.S.A.||[https://pubmed.ncbi.nlm.nih.gov/36095197  36095197 ]||[https://flybase.org/reports/FBrf0254485 FBrf0254485]
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==== Aug 2022====
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{| class="wikitable"
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! ''Author description of technical advance''!!''Title''!!''Journal''!!''PubMed ID''!! ''FBrf number''
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| A self-supervised deep learning method to analyze fly behaviors.||Selfee, self-supervised features extraction of animal behaviors.||eLife||[https://pubmed.ncbi.nlm.nih.gov/35708244  35708244 ]||[https://flybase.org/reports/FBrf0254056 FBrf0254056]
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| Aion is a bi-stable Anion-conducting Channelrhodopsin allowing sustained silencing of neuronal activity. Aion can be activated with a short blue light pulse (open state half-life ~15min), which can be reversed using orange light.||Aion is a bistable anion-conducting channelrhodopsin that provides temporally extended and reversible neuronal silencing.||Commun. Biol.||[https://pubmed.ncbi.nlm.nih.gov/35810216  35810216 ]||[https://flybase.org/reports/FBrf0253932 FBrf0253932]
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| Positive Cell Cluster Detection method; a devoloped method aims to link the expression of a given transcription factor to the birth-order of an immature motoneuron by using the correlation between the birth-order of motoneuron and their spatial organization.||Post-transcriptional regulation of transcription factor codes in immature neurons drives neuronal diversity.||Cell Rep.||[https://pubmed.ncbi.nlm.nih.gov/35767953  35767953 ]||[https://flybase.org/reports/FBrf0253867 FBrf0253867]
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| Expression of different heat shock proteins during defined stages progression of epithelial malignant tumors of different genetic backgrounds.||Elevation of major constitutive heat shock proteins is heat shock factor independent and essential for establishment and growth of Lgl loss and Yorkie gain-mediated tumors in Drosophila.||Cell Stress Chaperones||[https://pubmed.ncbi.nlm.nih.gov/35704239  35704239 ]||[https://flybase.org/reports/FBrf0254080 FBrf0254080]
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| Spermatogenic single-cyst RNA-seq data, including mitotic, meiotic and post-meiotic stages, of D. melanogaster and D. simulans were presented in this paper, which could be an informative resource to those interested in development, expression evolution, etc.||Spatiotemporal Regulation of a Single Adaptively Evolving Trans-Regulatory Element Contributes to Spermatogenetic Expression Divergence in Drosophila.||Mol. Biol. Evol.||[https://pubmed.ncbi.nlm.nih.gov/35687719  35687719 ]||[https://flybase.org/reports/FBrf0254010 FBrf0254010]
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| deGRadFP construct for targeted degradation of GFP-fusion proteins in freshly laid eggs.||Female meiosis II and pronuclear fusion require the microtubule transport factor Bicaudal D.||Development||[https://pubmed.ncbi.nlm.nih.gov/35723263  35723263 ]||[https://flybase.org/reports/FBrf0253939 FBrf0253939]
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| Consensus docking.||Consensus combining outcomes of multiple ensemble dockings: examples using dDAT crystalized complexes.||MethodsX||[https://pubmed.ncbi.nlm.nih.gov/35935527  35935527 ]||[https://flybase.org/reports/FBrf0254184 FBrf0254184]
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| 1. Generation of a palmitoylome of S2R+ cell line cells 2. Use of BioID to identify interaction partners of DHHC-PAT proteins involved in protein S-palmitoylation.||The S-palmitoylome and DHHC-PAT interactome of Drosophila melanogaster S2R+ cells indicate a high degree of conservation to mammalian palmitoylomes.||PLoS ONE||[https://pubmed.ncbi.nlm.nih.gov/35960718  35960718 ]||[https://flybase.org/reports/FBrf0254250 FBrf0254250]
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| Complexome profiling.||CG7630 is the Drosophila melanogaster homolog of the cytochrome c oxidase subunit COX7B.||EMBO Rep.||[https://pubmed.ncbi.nlm.nih.gov/35699132  35699132 ]||[https://flybase.org/reports/FBrf0254233 FBrf0254233]
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| A bacterial gene encoding for a toxic protein (Kid) that can be used to ablate cells. ||A robust and tunable system for targeted cell ablation in developing embryos.||Dev. Cell||[https://pubmed.ncbi.nlm.nih.gov/35914525  35914525 ]||[https://flybase.org/reports/FBrf0254323 FBrf0254323]
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| Antibodies.||Single amino-acid mutation in a Drosophila melanogaster ribosomal protein: An insight in uL11 transcriptional activity.||PLoS ONE||[https://pubmed.ncbi.nlm.nih.gov/35981051  35981051 ]||[https://flybase.org/reports/FBrf0254298 FBrf0254298]
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| 3C method for Drosophila larvae.||Application of the 3C Method to Study the Developmental Genes in Drosophila Larvae.||Front. Genet.||[https://pubmed.ncbi.nlm.nih.gov/35910225  35910225 ]||[https://flybase.org/reports/FBrf0254079 FBrf0254079]
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==== Jul 2022====
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{| class="wikitable"
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! ''Author description of technical advance''!!''Title''!!''Journal''!!''PubMed ID''!! ''FBrf number''
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| R-loop mapping in embryos and S2 cells.||R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures.||J. Mol. Biol.||[https://pubmed.ncbi.nlm.nih.gov/35609632  35609632 ]||[https://flybase.org/reports/FBrf0253819 FBrf0253819]
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| Generation of CRISPR/Cas13 plasmids (RxCas13d and PspCas13b) for use in Drosophila.||CRISPR/Cas13 effectors have differing extents of off-target effects that limit their utility in eukaryotic cells.||Nucleic Acids Res.||[https://pubmed.ncbi.nlm.nih.gov/35244715  35244715 ]||[https://flybase.org/reports/FBrf0253797 FBrf0253797]
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| Genome edited mutant in the dorsal gene created by CRISPR Cas9 genome editing.||SUMOylation of Dorsal attenuates Toll/NF-κB signaling.||Genetics||[https://pubmed.ncbi.nlm.nih.gov/35567478  35567478 ]||[https://flybase.org/reports/FBrf0253870 FBrf0253870]
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| We developed a method to quantitate the number and cell body position of cell types within organs by combining fluorescent histone fusion reporters, light sheet microscopy and computational tools. ||Intact Drosophila central nervous system cellular quantitation reveals sexual dimorphism.||eLife||[https://pubmed.ncbi.nlm.nih.gov/35801638  35801638 ]||[https://flybase.org/reports/FBrf0253944 FBrf0253944]
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| We demonstrated that tissue-specific knockout in parallel with rescue of the knockout by cDNA expression by using the sgRNAs targeting the exon-intron junction of target genes. The sgRNAs/Cas9 cleave the genomic locus of the genes, but not UAS-cDNA transgenes. ||CRISPR/Cas9-mediated tissue-specific knockout and cDNA rescue using sgRNAs that target exon-intron junctions in Drosophila melanogaster.||STAR Protoc||[https://pubmed.ncbi.nlm.nih.gov/35719725  35719725 ]||[https://flybase.org/reports/FBrf0253824 FBrf0253824]
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==== Jun 2022====
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! ''Author description of technical advance''!!''Title''!!''Journal''!!''PubMed ID''!! ''FBrf number''
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| NanoDam is a novel technique enables rapid cell type specific, genome-wide profiling of protein-DNA interactions with high temporal and spatial resolution in a single genetic cross.||NanoDam identifies Homeobrain (ARX) and Scarecrow (NKX2.1) as conserved temporal factors in the Drosophila central brain and visual system.||Dev. Cell||[https://pubmed.ncbi.nlm.nih.gov/35483359  35483359 ]||[https://flybase.org/reports/FBrf0253373 FBrf0253373]
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| We developed a new technique that allow the detection of extracellular ROS ( H2O2) in the Drosophila midgut.||Integrin-ECM interactions and membrane-associated Catalase cooperate to promote resilience of the Drosophila intestinal epithelium.||PLoS Biol.||[https://pubmed.ncbi.nlm.nih.gov/35522719  35522719 ]||[https://flybase.org/reports/FBrf0253528 FBrf0253528]
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| We generated new reagents for the field, please refer to the paper for the reagents generated.||Auxilin regulates intestinal stem cell proliferation through EGFR.||Stem Cell Reports||[https://pubmed.ncbi.nlm.nih.gov/35427486  35427486 ]||[https://flybase.org/reports/FBrf0253455 FBrf0253455]
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| We generated new reagents for the field, please refer to the paper for the reagents generated.||Phosphorylation of Yun is required for stem cell proliferation and tumorigenesis.||Cell Prolif||[https://pubmed.ncbi.nlm.nih.gov/35437864  35437864 ]||[https://flybase.org/reports/FBrf0253603 FBrf0253603]
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| This protocol paper describes how to differentially purify cytoplasmic and nuclear ribonucleoprotein (RNP) complexes from adult Drosophila heads.||An RNA-immunoprecipitation protocol to identify RNAs associated with RNA-binding proteins in cytoplasmic and nuclear Drosophila head fractions.||STAR Protoc||[https://pubmed.ncbi.nlm.nih.gov/35634357  35634357 ]||[https://flybase.org/reports/FBrf0253600 FBrf0253600]
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| Here, we described and characterized a low-cost, easy-to-construct device to enable students to record rapid Drosophila melanogaster (fruit fly) behaviors during optogenetics experiments. ||An optogenetics device with smartphone video capture to introduce neurotechnology and systems neuroscience to high school students.||PLoS ONE||[https://pubmed.ncbi.nlm.nih.gov/35522662  35522662 ]||[https://flybase.org/reports/FBrf0253392 FBrf0253392]
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| Isolation and quantitatvie analysis of fly cuticular microbiotas.||Microbiome assembly on Drosophila body surfaces benefits the flies to combat fungal infections.||iScience||[https://pubmed.ncbi.nlm.nih.gov/35663020  35663020 ]||[https://flybase.org/reports/FBrf0253684 FBrf0253684]
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| All-optical approach to study olfactory system and glomeruli: optogenetic activation of glomeruli and calcium imaging readout.||All-optical manipulation of the Drosophila olfactory system.||Sci. Rep.||[https://pubmed.ncbi.nlm.nih.gov/35595846  35595846 ]||[https://flybase.org/reports/FBrf0253539 FBrf0253539]
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| Nuclear Matrix (NuMat) is a biochemically defined entity that provides a snap shot of the features of nuclear architecture. Here we present a protocol to isolate and visualize NuMat in situ in intact embryos or tissues of Drosophila melanogaster and its applications. ||In situ Nuclear Matrix preparation in Drosophila melanogaster enabling genetic analysis of the nuclear architecture.||STAR Protoc||[https://pubmed.ncbi.nlm.nih.gov/35600936  35600936 ]||[https://flybase.org/reports/FBrf0253551 FBrf0253551]
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| Hi speed planar illumination microscopy.||Regulation of PDF receptor signaling controlling daily locomotor rhythms in Drosophila.||PLoS Genet.||[https://pubmed.ncbi.nlm.nih.gov/35605015  35605015 ]||[https://flybase.org/reports/FBrf0253689 FBrf0253689]
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|-
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| CRISPR-Cas9 genome editing was used to create a new sog knock out mutant in which the sog 5' untranslated region was partially removed, along with sequence encoding the sog start codon and signal peptide, which were replaced with an attP recombination sequence (sogattP). ||Modelling the structure of Short Gastrulation and generation of a toolkit for studying its function in Drosophila.||Biol. Open||[https://pubmed.ncbi.nlm.nih.gov/35603711  35603711 ]||[https://flybase.org/reports/FBrf0253731 FBrf0253731]
 +
|- bgcolor="lightgrey"
 +
| In this study we describe SpyChIP, which depends on covalent isopeptide bond between two peptides SpyTag and SpyCatcher, to identify sites of cell type-specific transcription factor (TF) occupancy in native physiological contexts without tissue dissociation or nuclei sorting. ||SpyChIP identifies cell type-specific transcription factor occupancy from complex tissues.||Proc. Natl. Acad. Sci. U.S.A.||[https://pubmed.ncbi.nlm.nih.gov/35696584  35696584 ]||[https://flybase.org/reports/FBrf0253726 FBrf0253726]
 +
|-
 +
| Live imaging of ex-vivo testis with DNA and lysosome markers to explore phagoptosis.||The phagocytic cyst cells in Drosophila testis eliminate germ cell progenitors via phagoptosis.||Sci. Adv.||[https://pubmed.ncbi.nlm.nih.gov/35714186  35714186 ]||[https://flybase.org/reports/FBrf0253775 FBrf0253775]
 +
|- bgcolor="lightgrey"
 +
| We developed a system modeling early neurodegenerative events in Drosophila adult photoreceptor cells. Thanks to the stereotypy of their axonal projections, this system delivers quantitative data on sporadic and progressive axonal degeneration of photoreceptor cells. ||A Quantitative Model of Sporadic Axonal Degeneration in the Drosophila Visual System.||J. Neurosci.||[https://pubmed.ncbi.nlm.nih.gov/35534228  35534228 ]||[https://flybase.org/reports/FBrf0253774 FBrf0253774]
 +
|-
 +
|}
 +
 
 +
==== May 2022====
 +
{| class="wikitable"
 +
|-
 +
! ''Author description of technical advance''!!''Title''!!''Journal''!!''PubMed ID''!! ''FBrf number''
 +
|-
 +
| New fluorescent phenotypic markers. Balancer chromosomes for Drosophila simulans.||Transgenic tools for targeted chromosome rearrangements allow construction of balancer chromosomes in non-melanogaster Drosophila species.||G3 (Bethesda)||[https://pubmed.ncbi.nlm.nih.gov/35143616  35143616 ]||[https://flybase.org/reports/FBrf0253138 FBrf0253138]
 +
|- bgcolor="lightgrey"
 +
| The paper offers a computational model that recreates the posterior localization of nanos and polar granule component mRNAs in the oocyte and early embryo. ||Computational modeling offers new insight into Drosophila germ granule development.||Biophys. J.||[https://pubmed.ncbi.nlm.nih.gov/35288123  35288123 ]||[https://flybase.org/reports/FBrf0253258 FBrf0253258]
 +
|-
 +
| Measurement of mitochondrial respiratory chain enzymatic activities in D. melanogaster samples.||Measurement of mitochondrial respiratory chain enzymatic activities in Drosophila melanogaster samples.||STAR Protoc||[https://pubmed.ncbi.nlm.nih.gov/35479112  35479112 ]||[https://flybase.org/reports/FBrf0253336 FBrf0253336]
 +
|- bgcolor="lightgrey"
 +
| iPOND identification of replication fork associated proteins in 3-5h embryos and S2 cell lines by quantitative mass spectrometry.||Identification of replication fork-associated proteins in Drosophila embryos and cultured cells using iPOND coupled to quantitative mass spectrometry.||Sci. Rep.||[https://pubmed.ncbi.nlm.nih.gov/35484306  35484306 ]||[https://flybase.org/reports/FBrf0253333 FBrf0253333]
 +
|-
 +
| Our paper describes HyDrop, a completely open-source droplet-microfluidic single-cell sequencing method. HyDrop can work in scRNA-seq or scATAC-seq mode, and has been tested on human, mouse and drosophila samples.||Hydrop enables droplet-based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads.||eLife||[https://pubmed.ncbi.nlm.nih.gov/35195064  35195064 ]||[https://flybase.org/reports/FBrf0253117 FBrf0253117]
 +
|- bgcolor="lightgrey"
 +
| We describe optimized assay for transposase-accessible chromatin by sequencing (ATAC-seq) library preparation using nuclei isolated from adult Drosophila brains. This optimized protocol will facilitate future ATAC-seq studies using adult flies.||Optimized assay for transposase-accessible chromatin by sequencing (ATAC-seq) library preparation from adult Drosophila melanogaster neurons.||Sci. Rep.||[https://pubmed.ncbi.nlm.nih.gov/35411004  35411004 ]||[https://flybase.org/reports/FBrf0253212 FBrf0253212]
 +
|-
 +
| Two new mutant alleles, Yippee[Chi-A] (BL#93858) and Yippee[Delta1] (BL#93859).||A fly appeared: sable, a classic Drosophila mutation, maps to Yippee, a gene affecting body color, wings, and bristles.||G3 (Bethesda)||[https://pubmed.ncbi.nlm.nih.gov/35266526  35266526 ]||[https://flybase.org/reports/FBrf0253414 FBrf0253414]
 +
|- bgcolor="lightgrey"
 +
| Development of a CRISPR/Cas9-based knock-in method to target genes in the Drosophila genome.  We also present an updated antennal lobe atlas based on our findings. ||Chemoreceptor co-expression in Drosophila melanogaster olfactory neurons.||eLife||[https://pubmed.ncbi.nlm.nih.gov/35442190  35442190 ]||[https://flybase.org/reports/FBrf0253272 FBrf0253272]
 +
|-
 +
| New plasmid and Drosophila lines to overexpress transgenes in Drosophila.||A LexAop > UAS > QUAS trimeric plasmid to generate inducible and interconvertible Drosophila overexpression transgenes.||Sci. Rep.||[https://pubmed.ncbi.nlm.nih.gov/35264662  35264662 ]||[https://flybase.org/reports/FBrf0252918 FBrf0252918]
 +
|- bgcolor="lightgrey"
 +
| Single-cell wounding model, epidermis.||Calcium bursts allow rapid reorganization of EFhD2/Swip-1 cross-linked actin networks in epithelial wound closure.||Nat. Commun.||[https://pubmed.ncbi.nlm.nih.gov/35524157  35524157 ]||[https://flybase.org/reports/FBrf0253404 FBrf0253404]
 +
|-
 +
| Automated, high-resolution quantitative phenotyping of Drosophila intestines based on cell segmentation data. Using cell coordinates, the intestines are computationally linearized and aligned to enable comparative analysis along their whole length.||An image analysis method for regionally defined cellular phenotyping of the Drosophila midgut.||Cell Rep Methods||[https://pubmed.ncbi.nlm.nih.gov/35474669  35474669 ]||[https://flybase.org/reports/FBrf0253351 FBrf0253351]
 +
|- bgcolor="lightgrey"
 +
| The effect of Patronin-RNAi on the microtubule polarity of Class 4 neurons can be assayed using the recombinant line: ppk-gal4, UAS-EB1-TagRFP-T, UAS-Patronin-RNAi (BL36659)/TM6. ||Microtubule polarity is instructive for many aspects of neuronal polarity.||Dev. Biol.||[https://pubmed.ncbi.nlm.nih.gov/35341730  35341730 ]||[https://flybase.org/reports/FBrf0253310 FBrf0253310]
 +
|-
 +
| UAS-NCDN (Neurochondrin) transgenic flies.||Regulation of the evolutionarily conserved muscle myofibrillar matrix by cell type dependent and independent mechanisms.||Nat. Commun.||[https://pubmed.ncbi.nlm.nih.gov/35562354  35562354 ]||[https://flybase.org/reports/FBrf0253445 FBrf0253445]
 +
|- bgcolor="lightgrey"
 +
| A new anti-Frl antibody was generated in rat after immunization with a purified recombinant protein containing the amino acid residues 687-1183 of Frl.||A Comparative Study of the Role of Formins in Drosophila Embryonic Dorsal Closure.||Cells||[https://pubmed.ncbi.nlm.nih.gov/35563844  35563844 ]||[https://flybase.org/reports/FBrf0253495 FBrf0253495]
 +
|-
 +
|}
 +
 
 +
==== Apr 2022====
 +
{| class="wikitable"
 +
|-
 +
! ''Author description of technical advance''!!''Title''!!''Journal''!!''PubMed ID''!! ''FBrf number''
 +
|-
 +
| This paper utilizes FIJI macros to quantify cachectic phenotypes such as muscle detachment and lipid droplet size.||Analyzing cachectic phenotypes in the muscle and fat body of Drosophila larvae.||STAR Protoc||[https://pubmed.ncbi.nlm.nih.gov/35284841  35284841 ]||[https://flybase.org/reports/FBrf0252884 FBrf0252884]
 +
|- bgcolor="lightgrey"
 +
| SoAL: tool for social behavior analysis. SDPD-15k: fly social behavior training dataset for SoAL.  MIAS: software for video acquisition. ||Behavioral signatures of structured feature detection during courtship in Drosophila.||Curr. Biol.||[https://pubmed.ncbi.nlm.nih.gov/35139360  35139360 ]||[https://flybase.org/reports/FBrf0253010 FBrf0253010]
 +
|-
 +
| This paper reports a CRISPR/Cas9 edited genomic mutant of Jra (FBgn0001291) resistant to SUMO conjugation on Lysines 29 and 190. The resultant fly line shows a phenotype consistent with increased activity of Jra. ||SUMOylation of Jun fine-tunes the Drosophila gut immune response.||PLoS Pathog.||[https://pubmed.ncbi.nlm.nih.gov/35255103  35255103 ]||[https://flybase.org/reports/FBrf0252954 FBrf0252954]
 +
|- bgcolor="lightgrey"
 +
| We generated new reagents for the field, please refer to the paper for the reagents generated.||Derlin-1 and TER94/VCP/p97 are required for intestinal homeostasis.||J. Genet. Genomics||[https://pubmed.ncbi.nlm.nih.gov/34547438  34547438 ]||[https://flybase.org/reports/FBrf0253107 FBrf0253107]
 +
|-
 +
| 6 strains were created or customized for enabling recombination on the 4th chromosome.||New resources for the Drosophila 4th chromosome: FRT101F enabled mitotic clones and Bloom syndrome helicase enabled meiotic recombination.||G3 (Bethesda)||[https://pubmed.ncbi.nlm.nih.gov/35084488  35084488 ]||[https://flybase.org/reports/FBrf0253111 FBrf0253111]
 +
|- bgcolor="lightgrey"
 +
| New resource: measured synaptic surface areas in a variety of neurons in the Drosophila first instar larval central nervous system.||Synaptic counts approximate synaptic contact area in Drosophila.||PLoS ONE||[https://pubmed.ncbi.nlm.nih.gov/35377898  35377898 ]||[https://flybase.org/reports/FBrf0253082 FBrf0253082]
 +
|-
 +
| Tracking of larval locomotion for long periods.||Long-Term Observation of Locomotion of Drosophila Larvae Facilitates Feasibility of Food-Choice Assays.||Adv Biol (Weinh)||[https://pubmed.ncbi.nlm.nih.gov/34365739  34365739 ]||[https://flybase.org/reports/FBrf0253215 FBrf0253215]
 +
|- bgcolor="lightgrey"
 +
| S2R+ cells with stable "LiveDrop" reporters (GFP and mRFP)  that marks the surface of lipid droplets. ||Recruitment of Peroxin 14 to lipid droplets affects lipid storage in Drosophila.||J. Cell Sci.||[https://pubmed.ncbi.nlm.nih.gov/35274690  35274690 ]||[https://flybase.org/reports/FBrf0253163 FBrf0253163]
 +
|-
 +
| Automated pipeline for quantifying interactions between adjacent glial subsets.||Quantifying Glial-Glial Tiling Using Automated Image Analysis in Drosophila.||Front. Cell. Neurosci.||[https://pubmed.ncbi.nlm.nih.gov/35401121  35401121 ]||[https://flybase.org/reports/FBrf0253225 FBrf0253225]
 +
|- bgcolor="lightgrey"
 +
| Behavioral method for measuring solid food consumption.||Identification of additional dye tracers for measuring solid food intake and food preference via consumption-excretion in Drosophila.||Sci. Rep.||[https://pubmed.ncbi.nlm.nih.gov/35418664  35418664 ]||[https://flybase.org/reports/FBrf0253152 FBrf0253152]
 +
|-
 +
|}
 +
 
 +
==== Mar 2022====
 +
{| class="wikitable"
 +
|-
 +
! ''Author description of technical advance''!!''Title''!!''Journal''!!''PubMed ID''!! ''FBrf number''
 +
|-
 +
| Modified TUNEL protocol to study cell death in tissues.||Protocol to study cell death using TUNEL assay in Drosophila imaginal discs.||STAR Protoc||[https://pubmed.ncbi.nlm.nih.gov/35128481  35128481 ]||[https://flybase.org/reports/FBrf0252563 FBrf0252563]
 +
|- bgcolor="lightgrey"
 +
| We developed a PCR-based NGS protocol to cluster cell lines based on the genome-wide distribution of a limited number of diagnostic TE families. It can accurately identify and authenticate the numerous Drosophila cell lines.||A novel transposable element-based authentication protocol for Drosophila cell lines.||G3 (Bethesda)||[https://pubmed.ncbi.nlm.nih.gov/34849844  34849844 ]||[https://flybase.org/reports/FBrf0252561 FBrf0252561]
 +
|-
 +
| It is improvement on culturing wing imaginal disc and live imaging cytonemes, specially the ones from the Air Sac Primordium. It also contains a follow up Cytoneme Dynamics analysis tool for ImageJ/FIJI and a R/RStudios pipeline for the data analysis and graphical representation.||Protocol for ex vivo time lapse imaging of Drosophila melanogaster cytonemes.||STAR Protoc||[https://pubmed.ncbi.nlm.nih.gov/35141564  35141564 ]||[https://flybase.org/reports/FBrf0252689 FBrf0252689]
 +
|- bgcolor="lightgrey"
 +
| Use of DLM spiking readouts. ||Distinct Aging-Vulnerable and -Resilient Trajectories of Specific Motor Circuit Functions in Oxidation- and Temperature-Stressed Drosophila.||eNeuro||[https://pubmed.ncbi.nlm.nih.gov/34876473  34876473 ]||[https://flybase.org/reports/FBrf0252428 FBrf0252428]
 +
|-
 +
| We developed a CRISPR/Cas9-based knockin system (LexA.G4HACK) to replace Gal4 coding sequences with LexA, and a LexAop-based short hairpin RNA expression vector (pWALEXA20) to achieve short hairpin RNA-mediated gene silencing.||Transgenic Drosophila lines for LexA-dependent gene and growth regulation.||G3 (Bethesda)||[https://pubmed.ncbi.nlm.nih.gov/35100369  35100369 ]||[https://flybase.org/reports/FBrf0252870 FBrf0252870]
 +
|- bgcolor="lightgrey"
 +
| A new high-speed imaging method to record ultra-fast photomechanical photoreceptor microsaccades in living flies.||High-speed imaging of light-induced photoreceptor microsaccades in compound eyes.||Commun. Biol.||[https://pubmed.ncbi.nlm.nih.gov/35241794  35241794 ]||[https://flybase.org/reports/FBrf0252822 FBrf0252822]
 +
|-
 +
| NMR-based profiling of polar and non-polar metabolites in dissected larval tissues or whole animals.||A toolbox to study metabolic status of Drosophila melanogaster larvae.||STAR Protoc||[https://pubmed.ncbi.nlm.nih.gov/35252884  35252884 ]||[https://flybase.org/reports/FBrf0252824 FBrf0252824]
 +
|- bgcolor="lightgrey"
 +
| Deep single-cell ATAC-seq dataset of mesoderm / muscle cell fate during embryonic development.||Simultaneous cellular and molecular phenotyping of embryonic mutants using single-cell regulatory trajectories.||Dev. Cell||[https://pubmed.ncbi.nlm.nih.gov/35176234  35176234 ]||[https://flybase.org/reports/FBrf0252873 FBrf0252873]
 +
|-
 +
| We used a new CRISPR Drosophila tafazzin mutant line. This line has the first 889 basepairs removed from the first exon of the tafazzin gene. Additionally, this line has a RFP marker knocked in. ||NAD supplementation improves mitochondrial performance of cardiolipin mutants.||Biochim Biophys Acta Mol Cell Biol Lipids||[https://pubmed.ncbi.nlm.nih.gov/35051613  35051613 ]||[https://flybase.org/reports/FBrf0252704 FBrf0252704]
 +
|- bgcolor="lightgrey"
 +
| Real-time optical recording of the formation of a visual memory trace in the ellipsoid body.||Differential mechanisms underlie trace and delay conditioning in Drosophila.||Nature||[https://pubmed.ncbi.nlm.nih.gov/35173333  35173333 ]||[https://flybase.org/reports/FBrf0252922 FBrf0252922]
 +
|-
 +
| Reagents for new spliceform generated.||Septins tune lipid kinase activity and PI(4,5)P2 turnover during G-protein-coupled PLC signalling in vivo.||Life Sci Alliance||[https://pubmed.ncbi.nlm.nih.gov/35277468  35277468 ]||[https://flybase.org/reports/FBrf0252936 FBrf0252936]
 +
|- bgcolor="lightgrey"
 +
| The following are new resources generated in this paper. 1. Rat monoclonal anti-FruM antibody (clone 1C1) 2. Rat monoclonal anti-FruM antibody (clone 1A8) 3. Rat monoclonal anti-FruALL antibody (clone 2E4) 4. Rat monoclonal anti-FruALL antibody (clone 3G11D12).||Mutually exclusive expression of sex-specific and non-sex-specific fruitless gene products in the Drosophila central nervous system.||Gene Expr. Patterns||[https://pubmed.ncbi.nlm.nih.gov/35124238  35124238 ]||[https://flybase.org/reports/FBrf0252913 FBrf0252913]
 +
|-
 +
| High resolution microscopy and ultra-sensitive proteomics of nephrocytes.||Scaffold polarity proteins Par3A and Par3B share redundant functions while Par3B acts independent of atypical protein kinase C/Par6 in podocytes to maintain the kidney filtration barrier.||Kidney Int.||[https://pubmed.ncbi.nlm.nih.gov/34929254  34929254 ]||[https://flybase.org/reports/FBrf0252977 FBrf0252977]
 +
|- bgcolor="lightgrey"
 +
|}
 +
 
 +
==== Feb 2022====
 +
{| class="wikitable"
 +
|-
 +
! ''Author description of technical advance''!!''Title''!!''Journal''!!''PubMed ID''!! ''FBrf number''
 +
|-
 +
| Computational tools for the analysis of loosely-coupled patterns of neuronal activity and for detecting phases in the execution of rhythmic behaviors.||Extracting temporal relationships between weakly coupled peptidergic and motoneuronal signaling: Application to Drosophila ecdysis behavior.||PLoS Comput. Biol.||[https://pubmed.ncbi.nlm.nih.gov/34910730  34910730 ]||[https://flybase.org/reports/FBrf0252232 FBrf0252232]
 +
|- bgcolor="lightgrey"
 +
| Stable Isotope Labelling of Amino Acids in Flies (SILAF) is a cost-effective and highly efficient SILAC technique, adapted to Drosophila laboratory needs. It is based on a holidic food source and achieves 99.5% labelling efficiency with heavy lysine at 15$ per mg of protein.||Stable Isotope Labeling of Amino Acids in Flies (SILAF) Reveals Differential Phosphorylation of Mitochondrial Proteins Upon Loss of OXPHOS Subunits.||Mol. Cell. Proteomics||[https://pubmed.ncbi.nlm.nih.gov/33640490  33640490 ]||[https://flybase.org/reports/FBrf0252195 FBrf0252195]
 +
|-
 +
| New Drosophila transgenic lines generated that can be available at request.||Selective autophagy controls innate immune response through a TAK1/TAB2/SH3PX1 axis.||Cell Rep.||[https://pubmed.ncbi.nlm.nih.gov/35081354  35081354 ]||[https://flybase.org/reports/FBrf0252505 FBrf0252505]
 +
|- bgcolor="lightgrey"
 +
| We have developed allelic drive based transgenic fly that can target the insecticide resistant para 1014F locus.  We have also developed a fly line containing 3xP3GFP insertion at para L1014 locus. ||Reversing insecticide resistance with allelic-drive in Drosophila melanogaster.||Nat. Commun.||[https://pubmed.ncbi.nlm.nih.gov/35022402  35022402 ]||[https://flybase.org/reports/FBrf0252383 FBrf0252383]
 +
|-
 +
| This paper reports a new direct-drive btl-GFP reporter that can be used to follow tracheal morphology independently of the GAL4/UAS system.||A direct-drive GFP reporter for studies of tracheal development in Drosophila.||Fly||[https://pubmed.ncbi.nlm.nih.gov/35094652  35094652 ]||[https://flybase.org/reports/FBrf0252525 FBrf0252525]
 +
|- bgcolor="lightgrey"
 +
| This manuscript describes the use of micro-computerized tomography (microCT) for measuring the size and morphology of the Drosophila heart. This technique is especially useful for analyzing cardiac hypertrophy in flies.||Analysis of Drosophila cardiac hypertrophy by microcomputerized tomography for genetic dissection of heart growth mechanisms.||Am J Physiol Heart Circ Physiol||[https://pubmed.ncbi.nlm.nih.gov/34951542  34951542 ]||[https://flybase.org/reports/FBrf0252376 FBrf0252376]
 +
|-
 +
| Additions to FlyAtlas 2, Drosophila melanogaster gene expression resource: 1. Profile Search facility, 2. Category Search facility, 3. Additional Tissues, 4. Specialized section on larval midgut pH regions.||FlyAtlas 2 in 2022: enhancements to the Drosophila melanogaster expression atlas.||Nucleic Acids Res.||[https://pubmed.ncbi.nlm.nih.gov/34718735  34718735 ]||[https://flybase.org/reports/FBrf0252311 FBrf0252311]
 +
|- bgcolor="lightgrey"
 +
| A new resource: The mRNA expression (bulk RNA sequencing) of third instar larval ovaries (wild type-Oregon R) through three developmental time points. In addition the mRNA expression of somatic and germ line tissue (separated through Flow sorting) of the ovary in these stages.||Distinct gene expression dynamics in germ line and somatic tissue during ovariole morphogenesis in Drosophila melanogaster.||G3 (Bethesda)||[https://pubmed.ncbi.nlm.nih.gov/34849771  34849771 ]||[https://flybase.org/reports/FBrf0252584 FBrf0252584]
 +
|-
 +
| Python-based code used to quantify object-to-object distances; e.g., mRNA to centrosomes.||Drosophila centrocortin is dispensable for centriole duplication but contributes to centrosome separation.||G3 (Bethesda)||[https://pubmed.ncbi.nlm.nih.gov/35100335  35100335 ]||[https://flybase.org/reports/FBrf0252569 FBrf0252569]
 +
|- bgcolor="lightgrey"
 +
| A versatile toolkit focused on piRNA biology and transposon biology that combines germline transgenic RNAi, GFP marker lines for key proteins of the piRNA pathway.||A genetic toolkit for studying transposon control in the Drosophila melanogaster ovary.||Genetics||[https://pubmed.ncbi.nlm.nih.gov/34718559  34718559 ]||[https://flybase.org/reports/FBrf0252592 FBrf0252592]
 +
|-
 +
| A new method for accessing ovarian maturation by quantifying the amount of yolk with YP1::GFP reporter.||Effects of Food and Temperature on Drosophila melanogaster Reproductive Dormancy as Revealed by Quantification of a GFP-Tagged Yolk Protein in the Ovary.||Front. Physiol.||[https://pubmed.ncbi.nlm.nih.gov/35046840  35046840 ]||[https://flybase.org/reports/FBrf0252438 FBrf0252438]
 +
|- bgcolor="lightgrey"
 +
| Characterization of the role of Naa40 in lipid metabolism in Drosophila, specifically in the larval fat body.||Histone acetyltransferase NAA40 modulates acetyl-CoA levels and lipid synthesis.||BMC Biol.||[https://pubmed.ncbi.nlm.nih.gov/35057804  35057804 ]||[https://flybase.org/reports/FBrf0252501 FBrf0252501]
 +
|-
 +
| Using NanoLuc Binary Technology, we first developed an assay to detect ligand-dependent heterodimerization of the ecdysone receptor (EcR) and retinoid X receptor (RXR) in HEK 293T cells. We also developed HEK293 cells that stably express Ecdysone Importer.||Rapid Assessment of Insect Steroid Hormone Entry Into Cultured Cells.||Front. Physiol.||[https://pubmed.ncbi.nlm.nih.gov/35145429  35145429 ]||[https://flybase.org/reports/FBrf0252694 FBrf0252694]
 +
|- bgcolor="lightgrey"
 +
|}
 +
 
 +
==== Jan 2022====
 +
{| class="wikitable"
 +
|-
 +
! ''Author description of technical advance''!!''Title''!!''Journal''!!''PubMed ID''!! ''FBrf number''
 +
|-
 +
| Development of an automated microinjection system for Drosophila embryos.||Multiscale, multi-perspective imaging assisted robotic microinjection of 3D biological structures.||Annu Int Conf IEEE Eng Med Biol Soc||[https://pubmed.ncbi.nlm.nih.gov/34892294  34892294 ]||[https://flybase.org/reports/FBrf0252055 FBrf0252055]
 +
|- bgcolor="lightgrey"
 +
| We provide two macros to quantify exosome release and autophagy in the Drosophila Neuromuscular junction.||Macros to Quantify Exosome Release and Autophagy at the Neuromuscular Junction of Drosophila Melanogaster.||Front. Cell Dev. Biol.||[https://pubmed.ncbi.nlm.nih.gov/34869373  34869373 ]||[https://flybase.org/reports/FBrf0252025 FBrf0252025]
 +
|-
 +
| The transgenic flies overexpress dEGFR specifically within somatic intestinal stem cells (ISC) and enteroblasts (using the EsgGal4, GFP driver).||Membrane therapy using DHA suppresses epidermal growth factor receptor signaling by disrupting nanocluster formation.||J. Lipid Res.||[https://pubmed.ncbi.nlm.nih.gov/33515553  33515553 ]||[https://flybase.org/reports/FBrf0252238 FBrf0252238]
 +
|- bgcolor="lightgrey"
 +
| Genome sequences for D. suzukii individuals and population genomics analysis.||Population genomics of Drosophila suzukii reveal longitudinal population structure and signals of migrations in and out of the continental United States.||G3 (Bethesda)||[https://pubmed.ncbi.nlm.nih.gov/34599814  34599814 ]||[https://flybase.org/reports/FBrf0252078 FBrf0252078]
 +
|-
 +
| Cell line authentication using transposable element insertions.||Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture.||Genetics||[https://pubmed.ncbi.nlm.nih.gov/34849875  34849875 ]||[https://flybase.org/reports/FBrf0252038 FBrf0252038]
 +
|- bgcolor="lightgrey"
 +
| Utilizing a "lab-in-a-box" mechanism to increase accessibility of research opportunities for undergraduates.||Flying in the Face of Adversity: a Drosophila-Based Virtual CURE (Course-Based Undergraduate Research Experience) Provides a Semester-Long Authentic Research Opportunity to the Flipped Classroom.||J. Microbiol. Biol. Educ.||[https://pubmed.ncbi.nlm.nih.gov/34880963  34880963 ]||[https://flybase.org/reports/FBrf0252050 FBrf0252050]
 +
|-
 +
| Single molecule localization microscopy to visualize SNAP and HALO-tagged endogenous protein in tissue samples. Using the LifeAct peptide for super-resolution imaging of actin organization.||A single-molecule localization microscopy method for tissues reveals nonrandom nuclear pore distribution in Drosophila.||J. Cell Sci.||[https://pubmed.ncbi.nlm.nih.gov/34806753  34806753 ]||[https://flybase.org/reports/FBrf0252184 FBrf0252184]
 +
|- bgcolor="lightgrey"
 +
| GRO-Seq of Stage 5 Drosophila melanogaster embryos is included in the paper. We believe this would be a useful resource for other researchers.||Histone variant H2A.Z regulates zygotic genome activation.||Nat. Commun.||[https://pubmed.ncbi.nlm.nih.gov/34853314  34853314 ]||[https://flybase.org/reports/FBrf0252039 FBrf0252039]
 +
|-
 +
| Using mt-keima, we tried to analyze the incidence of mitophagy in Keyon cells.||Mitochondrial aconitase 1 regulates age-related memory impairment via autophagy/mitophagy-mediated neural plasticity in middle-aged flies.||Aging Cell||[https://pubmed.ncbi.nlm.nih.gov/34799973  34799973 ]||[https://flybase.org/reports/FBrf0252217 FBrf0252217]
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| UAS-TM4SF.||Fos regulates macrophage infiltration against surrounding tissue resistance by a cortical actin-based mechanism in Drosophila.||PLoS Biol.||[https://pubmed.ncbi.nlm.nih.gov/34990456  34990456 ]||[https://flybase.org/reports/FBrf0252327 FBrf0252327]
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| We utilized the Dorsal-Eye Gal4 (DE-GAL4) to drive the exosome marker GFP-CD63 in the dorsal half of the eye imaginal discs. We detect the GFP-CD63 puncta in the morphogenetic furrow on the ventral side of the eye imaginal discs.||Dihydroceramide desaturase promotes the formation of intraluminal vesicles and inhibits autophagy to increase exosome production.||iScience||[https://pubmed.ncbi.nlm.nih.gov/34877496  34877496 ]||[https://flybase.org/reports/FBrf0252065 FBrf0252065]
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| Here we Analyze the integrity of oxidative phosphorylation complexes in Drosophila flight muscles.||Analyzing the integrity of oxidative phosphorylation complexes in Drosophila flight muscles.||STAR Protoc||[https://pubmed.ncbi.nlm.nih.gov/34977670  34977670 ]||[https://flybase.org/reports/FBrf0252164 FBrf0252164]
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===2021===
 
===2021===
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==== Dec 2021====
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! ''Author description of technical advance''!!''Title''!!''Journal''!!''PubMed ID''!! ''FBrf number''
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| We developed Bitbow, a highly efficient and easy-to-use multicolor labeling system suitable for neural lineage and morphological studies. Bitbow transgenic lines, with streamlined methods in sample prep, high-resolution imaging and analysis bring unprecedented resolution & scale.||Bitbow Enables Highly Efficient Neuronal Lineage Tracing and Morphology Reconstruction in Single Drosophila Brains.||Front. Neural Circuits||[https://pubmed.ncbi.nlm.nih.gov/34744636  34744636 ]||[https://flybase.org/reports/FBrf0251755 FBrf0251755]
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|- bgcolor="lightgrey"
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| Optogenetic constructs for light-triggered cyclic AMP production.||PACmn for improved optogenetic control of intracellular cAMP.||BMC Biol.||[https://pubmed.ncbi.nlm.nih.gov/34663304  34663304 ]||[https://flybase.org/reports/FBrf0251641 FBrf0251641]
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|-
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| Adaptation of FRET-based kinase sensor for AMPK for use in fly.||AMPK adapts metabolism to developmental energy requirement during dendrite pruning in Drosophila.||Cell Rep.||[https://pubmed.ncbi.nlm.nih.gov/34788610  34788610 ]||[https://flybase.org/reports/FBrf0251912 FBrf0251912]
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|- bgcolor="lightgrey"
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| UAS-human ORF as well as UAS-Drosophila ORF.||A cross-species approach for the identification of Drosophila male sterility genes.||G3 (Bethesda)||[https://pubmed.ncbi.nlm.nih.gov/34849808  34849808 ]||[https://flybase.org/reports/FBrf0252010 FBrf0252010]
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|-
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| Creation of cell lines with attP cassette at either 25C6 or 99F8 on the 2nd or 3rd chromosomes respectively and the successful RMCE with an associated attB plasmid tool kit.||Generation of Drosophila attP containing cell lines using CRISPR-Cas9.||G3 (Bethesda)||[https://pubmed.ncbi.nlm.nih.gov/33963853  33963853 ]||[https://flybase.org/reports/FBrf0251996 FBrf0251996]
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|- bgcolor="lightgrey"
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| The paper describes the expression of CS Chrimson and TRPA in motoneurons and how to apply patterned stimulation to evoke activity-dependent synaptic plasticity at the NMJ.||A comparison of three different methods of eliciting rapid activity-dependent synaptic plasticity at the Drosophila NMJ.||PLoS ONE||[https://pubmed.ncbi.nlm.nih.gov/34847197  34847197 ]||[https://flybase.org/reports/FBrf0251887 FBrf0251887]
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| New transgenic shRNA to KD oskar mRNA that is substantially more effective during oogenesis that previously available reagents.||Knock down analysis reveals critical phases for specific oskar noncoding RNA functions during Drosophila oogenesis.||G3 (Bethesda)||[https://pubmed.ncbi.nlm.nih.gov/34586387  34586387 ]||[https://flybase.org/reports/FBrf0252056 FBrf0252056]
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|- bgcolor="lightgrey"
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| Two genes conferring resistance to specific drugs are expressed in opposite sexes by incorporating sex-specific introns disrupting the coding sequences of drug-resistance genes. When the transgenic strain is raised on food supplemented with the corresponding drug, only individuals of the desired sex emerge.||A drug-inducible sex-separation technique for insects.||Nat. Commun.||[https://pubmed.ncbi.nlm.nih.gov/32355156  32355156 ]||[https://flybase.org/reports/FBrf0245511 FBrf0245511]
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|-
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| CLADES is a technology for cell lineage studies based on CRISPR-Cas9 technology that uses a system of genetic switches to activate and inactivate reporter genes.||A programmable sequence of reporters for lineage analysis.||Nat. Neurosci.||[https://pubmed.ncbi.nlm.nih.gov/32719561  32719561 ]||[https://flybase.org/reports/FBrf0247972 FBrf0247972]
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==== Nov 2021====
 
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Latest revision as of 08:26, 1 December 2022

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Overview

Authors of the papers listed below suggest that they include a technical advance, new type of reagent, or resource likely to be useful for other researchers. Author suggestions have been collected via the Fast-Track Your Paper tool since October 2020, with those most recently submitted at the top. Please note, there will be a lag time before listed papers can be found on FlyBase (FBrf links will become active when available) and the submission date does not necessarily match the publication date of the paper.

Technical Advances

2022

Nov 2022

Author description of technical advance Title Journal PubMed ID FBrf number
Endogenously tagged RNA polymerase II subunits, including mCherry-Rpb1 and EGFP-Rpb3. Coordinating transcription and replication to mitigate their conflicts in early Drosophila embryos. Cell Rep. 36261005 FBrf0254801
AO-SOLEIL mitigates deep tissue-induced deteriorations and was applied on dSTORM samples in adult Drosophila brains. A 2x improvement in the estimated axial localization precision with respect to widefield without aberration correction was observed. Adaptive optics in single objective inclined light sheet microscopy enables three-dimensional localization microscopy in adult Drosophila brains. Front. Neurosci. 36278016 FBrf0254788
(Z)-4-undecenal is the female pheromone of cosmopolitan D. melanogaster, an oxidation product of the aphrodisiac hydrocarbon (Z,Z)-7,11-heptacosadiene. Females of the Zimbabwe strain release also (Z)-4-nonenal, since they produce another hydrocarbon, (Z,Z)-5,9-heptacosadiene. The human odorant receptor OR10A6 is tuned to the pheromone of the commensal fruit fly Drosophila melanogaster. iScience 36300000 FBrf0254861
Population recordings of descending neurons during behavior. Descending neuron population dynamics during odor-evoked and spontaneous limb-dependent behaviors. eLife 36286408 FBrf0254871
Transgenes encoding HaloTag-based reporters for sparse labeling. HaloTag-based reporters for sparse labeling and cell tracking. Fly 36323649 FBrf0254955
Expression of different heat shock proteins during defined stages progression of epithelial malignant tumors of different genetic backgrounds. Delayed discovery of Hsp60 and subsequent characterization of moonlighting functions of multiple Hsp60 genes in Drosophila: a personal historical perspective. J. Genet. 36330787 FBrf0254951
We performed FRET data analysis using Matlab to visualize ATP concentration in living wing disc explants, then described the kinetics of FRET efficiency drop upon use of metabolic drugs targeting glycolysis and/or OxPhos in wt discs or discs with up/down-regulated Hh signaling. Hedgehog signaling can enhance glycolytic ATP production in the Drosophila wing disc. EMBO Rep. 36134875 FBrf0254957
Protocol for using bioluminescent bacteria to track infection. Longitudinal monitoring of individual infection progression in Drosophila melanogaster. iScience 36345341 FBrf0254928
In this paper, we made a high-quality and annotated sequencing of Drosophila nebulosa. In addition, we employed CRISPR/Cas9 to disrupt the White gene. This gene was found to be necessary for D. nebulosa mating. Nebulous without white: annotated long-read genome assembly and CRISPR/Cas9 genome engineering in Drosophila nebulosa. G3 (Bethesda) 36063049 FBrf0254926
New in silico model for cell-cell interaction for Hedgehog signaling. Predictive model for cytoneme guidance in Hedgehog signaling based on Ihog- Glypicans interaction. Nat. Commun. 36163184 FBrf0254595
RT&Tag uses antibodies to tether tagmentation reagents in situ in the nucleus for profiling of localized RNAs. The method has been used for profiling RNAs associated with silenced or active chromatin, or with RNA modifications. Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation. Nat. Methods 36192462 FBrf0254922
This paper describes a bioinformatics workflow designed to map insertions of natural transposons in genomes of interest with Genome ARTIST_v2, a software developed by our research team. Genome ARTIST_v2-An Autonomous Bioinformatics Tool for Annotation of Natural Transposons in Sequenced Genomes. Int. J. Mol. Sci. 36293549 FBrf0254901
We demonstrate stimulated Raman scattering spectro-microscopy driven by a multiple-plate continuum, enable spectroscopic interrogation across the entire Drosophila brain and electronic pre-resonance detection of a fluorescent dye. Towards stimulated Raman scattering spectro-microscopy across the entire Raman active region using a multiple-plate continuum. Opt. Express 36258449 FBrf0254804
Using 3D electron and light microscopy, we found the mitochondrial network distribution of Drosophila melanogaster strikingly similar to mouse cardiac and oxidative muscles. Proteomic analyses on indirect flight, jump, and leg muscles. Identification of evolutionarily conserved regulators of muscle mitochondrial network organization. Nat. Commun. 36333356 FBrf0254964
Optogenetic perturbation of aPKC in vivo, based on LARIAT system and GFP-aPKC knock-in line. aPKC regulates apical constriction to prevent tissue rupture in the Drosophila follicular epithelium. Curr. Biol. 36113470 FBrf0254903
Express Drosophila striated muscle myosin using Sf9/baculovirus system. Insect Sf9 cells are suitable for functional expression of insect, but not vertebrate, striated muscle myosin. Biochem. Biophys. Res. Commun. 36308905 FBrf0255002
A new stable 8X tissue expansion method and computational tools to reconstruct neural circuit structure in Drosophila using expansion microscopy. All tools are available on GitHub (https://github.com/JaneliaSciComp/exllsm-circuit-reconstruction). Rapid reconstruction of neural circuits using tissue expansion and light sheet microscopy. eLife 36286237 FBrf0255018
New model to analyse significant interactions from Hi-C and micro-C data. ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C data. Bioinformatics 35678507 FBrf0255007
A microfluidic microinjection technique and heartbeat quantification software were introduced which may help to perform cardiac toxicity studies. An in-vivo microfluidic assay reveals cardiac toxicity of heavy metals and the protective effect of metal responsive transcription factor (MTF-1) in Drosophila model. 3 Biotech 36275358 FBrf0254790

Oct 2022

Author description of technical advance Title Journal PubMed ID FBrf number
The paper describes a new muscle contraction model using Drosophila larvae and optogenetics. Modeling exercise using optogenetically contractible Drosophila larvae. BMC Genomics 36042416 FBrf0254389
Detailed description of tools for measuring cold tolerance under fictive cold stimuli via programmed optogenetic rearing. Protocols for measuring cold-evoked neural activity and cold tolerance in Drosophila larvae following fictive cold acclimation. STAR Protoc 35776643 FBrf0254520
LexAop transgenic lines and combining LexA and Gal4 together to study organ communication. Renal NF-κB activation impairs uric acid homeostasis to promote tumor-associated mortality independent of wasting. Immunity 36029766 FBrf0254493
An improved method of conducting genome-wide mapping of chromatin protein binding sites termed nanoCut&Run. The nanoCUT&RUN technique visualizes telomeric chromatin in Drosophila. PLoS Genet. 36048878 FBrf0254524
This paper identified variant PRC1 and PRC2.2 complexes in Drosophila using the BioTAP-XL technique. The previously unrecognized conservation of fly and mammalian PcG complexes provides a resource for improved understanding of epigenetic gene regulation in multicellular organisms. Variant Polycomb complexes in Drosophila consistent with ancient functional diversity. Sci. Adv. 36070387 FBrf0254426
This paper describes a new light-gated expression tool LOV-LexA, in which the transcription factor LexA is shuttled into the nucleus to drive expression of LexAop sequences in the presence of blue light (405nm wavelength) but remains in the cytoplasm in the dark. Spatial and temporal control of expression with light-gated LOV-LexA. G3 (Bethesda) 35876796 FBrf0254643
New reagent: iRFP-tagged His2Av. Near-infrared nuclear markers for Drosophila imaging. MicroPubl Biol 36212517 FBrf0254678
Allele dGao[47dsRed] is a platform for RMCE. Restoration of the GTPase activity and cellular interactions of Gαo mutants by Zn2+ in GNAO1 encephalopathy models. Sci. Adv. 36206333 FBrf0254662
We present tauLUM, a Drosophila model that leverages split- luciferase technology to assay tau multimerization in vivo. TauLUM is a powerful discovery platform for identifying genetic regulators and drugs targeting tau multimerization. TauLUM, an in vivo Drosophila sensor of tau multimerization, identifies neuroprotective interventions in tauopathy. Cell Rep Methods 36160048 FBrf0254597
This is an open access database for chromosome number and chromosome shape for Drosophila species and other dipterans. Diptera and Drosophila Karyotype Databases: A Useful Dataset to Guide Evolutionary and Genomic Studies. Front Ecol Evol 36238425 FBrf0254736

Sep 2022

Author description of technical advance Title Journal PubMed ID FBrf number
We used shotgun lipidomics and mass-spectrometry to analyze the impacts of vitamin A deficiency on the lipidome and the proteome of the Drosophila eye. Vitamin A Deficiency Alters the Phototransduction Machinery and Distinct Non-Vision-Specific Pathways in the Drosophila Eye Proteome. Biomolecules 36008977 FBrf0254376
Multichannel magnetothermal activation of heat sensors using iron oxide nanoparticles. Subsecond multichannel magnetic control of select neural circuits in freely moving flies. Nat. Mater. 35761060 FBrf0254201
Botulinum neurotoxin engineered for Gal4-mediated expression. When expressed in neurons, silences both evoked and spontaneous release. Botulinum neurotoxin accurately separates tonic vs. phasic transmission and reveals heterosynaptic plasticity rules in Drosophila. eLife 35993544 FBrf0254399
High resolution imaging of individual actin filaments in medioapical arrays in amnioserosa cells using grazing incidence, structured illumination. Superresolution microscopy reveals actomyosin dynamics in medioapical arrays. Mol. Biol. Cell 35544300 FBrf0254444
Hypoxia protocol. Standardized hypoxia-reoxygenation protocol to assess posthypoxic neurobehavioral impairments and molecular mechanisms in Drosophila melanogaster. STAR Protoc 36035795 FBrf0254331
Tools for effective control over the expression levels of transgenes are largely limited. We report a new series pUASTattB-based plasmids. These plasmids preserve the features of pUASTattB but contain a varying number of UAS sites. Generation and validation of pX-UASTattB for dose-dependent misexpression studies in Drosophila. MicroPubl Biol 36039330 FBrf0254375
Our study used a novel Rapamycin analog (Rapa* - 3Z) which specifically inhibits dTOR in presence of FKBP12-V55G mutant. Tissue-restricted inhibition of mTOR using chemical genetics. Proc. Natl. Acad. Sci. U.S.A. 36095197 FBrf0254485

Aug 2022

Author description of technical advance Title Journal PubMed ID FBrf number
A self-supervised deep learning method to analyze fly behaviors. Selfee, self-supervised features extraction of animal behaviors. eLife 35708244 FBrf0254056
Aion is a bi-stable Anion-conducting Channelrhodopsin allowing sustained silencing of neuronal activity. Aion can be activated with a short blue light pulse (open state half-life ~15min), which can be reversed using orange light. Aion is a bistable anion-conducting channelrhodopsin that provides temporally extended and reversible neuronal silencing. Commun. Biol. 35810216 FBrf0253932
Positive Cell Cluster Detection method; a devoloped method aims to link the expression of a given transcription factor to the birth-order of an immature motoneuron by using the correlation between the birth-order of motoneuron and their spatial organization. Post-transcriptional regulation of transcription factor codes in immature neurons drives neuronal diversity. Cell Rep. 35767953 FBrf0253867
Expression of different heat shock proteins during defined stages progression of epithelial malignant tumors of different genetic backgrounds. Elevation of major constitutive heat shock proteins is heat shock factor independent and essential for establishment and growth of Lgl loss and Yorkie gain-mediated tumors in Drosophila. Cell Stress Chaperones 35704239 FBrf0254080
Spermatogenic single-cyst RNA-seq data, including mitotic, meiotic and post-meiotic stages, of D. melanogaster and D. simulans were presented in this paper, which could be an informative resource to those interested in development, expression evolution, etc. Spatiotemporal Regulation of a Single Adaptively Evolving Trans-Regulatory Element Contributes to Spermatogenetic Expression Divergence in Drosophila. Mol. Biol. Evol. 35687719 FBrf0254010
deGRadFP construct for targeted degradation of GFP-fusion proteins in freshly laid eggs. Female meiosis II and pronuclear fusion require the microtubule transport factor Bicaudal D. Development 35723263 FBrf0253939
Consensus docking. Consensus combining outcomes of multiple ensemble dockings: examples using dDAT crystalized complexes. MethodsX 35935527 FBrf0254184
1. Generation of a palmitoylome of S2R+ cell line cells 2. Use of BioID to identify interaction partners of DHHC-PAT proteins involved in protein S-palmitoylation. The S-palmitoylome and DHHC-PAT interactome of Drosophila melanogaster S2R+ cells indicate a high degree of conservation to mammalian palmitoylomes. PLoS ONE 35960718 FBrf0254250
Complexome profiling. CG7630 is the Drosophila melanogaster homolog of the cytochrome c oxidase subunit COX7B. EMBO Rep. 35699132 FBrf0254233
A bacterial gene encoding for a toxic protein (Kid) that can be used to ablate cells. A robust and tunable system for targeted cell ablation in developing embryos. Dev. Cell 35914525 FBrf0254323
Antibodies. Single amino-acid mutation in a Drosophila melanogaster ribosomal protein: An insight in uL11 transcriptional activity. PLoS ONE 35981051 FBrf0254298
3C method for Drosophila larvae. Application of the 3C Method to Study the Developmental Genes in Drosophila Larvae. Front. Genet. 35910225 FBrf0254079

Jul 2022

Author description of technical advance Title Journal PubMed ID FBrf number
R-loop mapping in embryos and S2 cells. R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures. J. Mol. Biol. 35609632 FBrf0253819
Generation of CRISPR/Cas13 plasmids (RxCas13d and PspCas13b) for use in Drosophila. CRISPR/Cas13 effectors have differing extents of off-target effects that limit their utility in eukaryotic cells. Nucleic Acids Res. 35244715 FBrf0253797
Genome edited mutant in the dorsal gene created by CRISPR Cas9 genome editing. SUMOylation of Dorsal attenuates Toll/NF-κB signaling. Genetics 35567478 FBrf0253870
We developed a method to quantitate the number and cell body position of cell types within organs by combining fluorescent histone fusion reporters, light sheet microscopy and computational tools. Intact Drosophila central nervous system cellular quantitation reveals sexual dimorphism. eLife 35801638 FBrf0253944
We demonstrated that tissue-specific knockout in parallel with rescue of the knockout by cDNA expression by using the sgRNAs targeting the exon-intron junction of target genes. The sgRNAs/Cas9 cleave the genomic locus of the genes, but not UAS-cDNA transgenes. CRISPR/Cas9-mediated tissue-specific knockout and cDNA rescue using sgRNAs that target exon-intron junctions in Drosophila melanogaster. STAR Protoc 35719725 FBrf0253824

Jun 2022

Author description of technical advance Title Journal PubMed ID FBrf number
NanoDam is a novel technique enables rapid cell type specific, genome-wide profiling of protein-DNA interactions with high temporal and spatial resolution in a single genetic cross. NanoDam identifies Homeobrain (ARX) and Scarecrow (NKX2.1) as conserved temporal factors in the Drosophila central brain and visual system. Dev. Cell 35483359 FBrf0253373
We developed a new technique that allow the detection of extracellular ROS ( H2O2) in the Drosophila midgut. Integrin-ECM interactions and membrane-associated Catalase cooperate to promote resilience of the Drosophila intestinal epithelium. PLoS Biol. 35522719 FBrf0253528
We generated new reagents for the field, please refer to the paper for the reagents generated. Auxilin regulates intestinal stem cell proliferation through EGFR. Stem Cell Reports 35427486 FBrf0253455
We generated new reagents for the field, please refer to the paper for the reagents generated. Phosphorylation of Yun is required for stem cell proliferation and tumorigenesis. Cell Prolif 35437864 FBrf0253603
This protocol paper describes how to differentially purify cytoplasmic and nuclear ribonucleoprotein (RNP) complexes from adult Drosophila heads. An RNA-immunoprecipitation protocol to identify RNAs associated with RNA-binding proteins in cytoplasmic and nuclear Drosophila head fractions. STAR Protoc 35634357 FBrf0253600
Here, we described and characterized a low-cost, easy-to-construct device to enable students to record rapid Drosophila melanogaster (fruit fly) behaviors during optogenetics experiments. An optogenetics device with smartphone video capture to introduce neurotechnology and systems neuroscience to high school students. PLoS ONE 35522662 FBrf0253392
Isolation and quantitatvie analysis of fly cuticular microbiotas. Microbiome assembly on Drosophila body surfaces benefits the flies to combat fungal infections. iScience 35663020 FBrf0253684
All-optical approach to study olfactory system and glomeruli: optogenetic activation of glomeruli and calcium imaging readout. All-optical manipulation of the Drosophila olfactory system. Sci. Rep. 35595846 FBrf0253539
Nuclear Matrix (NuMat) is a biochemically defined entity that provides a snap shot of the features of nuclear architecture. Here we present a protocol to isolate and visualize NuMat in situ in intact embryos or tissues of Drosophila melanogaster and its applications. In situ Nuclear Matrix preparation in Drosophila melanogaster enabling genetic analysis of the nuclear architecture. STAR Protoc 35600936 FBrf0253551
Hi speed planar illumination microscopy. Regulation of PDF receptor signaling controlling daily locomotor rhythms in Drosophila. PLoS Genet. 35605015 FBrf0253689
CRISPR-Cas9 genome editing was used to create a new sog knock out mutant in which the sog 5' untranslated region was partially removed, along with sequence encoding the sog start codon and signal peptide, which were replaced with an attP recombination sequence (sogattP). Modelling the structure of Short Gastrulation and generation of a toolkit for studying its function in Drosophila. Biol. Open 35603711 FBrf0253731
In this study we describe SpyChIP, which depends on covalent isopeptide bond between two peptides SpyTag and SpyCatcher, to identify sites of cell type-specific transcription factor (TF) occupancy in native physiological contexts without tissue dissociation or nuclei sorting. SpyChIP identifies cell type-specific transcription factor occupancy from complex tissues. Proc. Natl. Acad. Sci. U.S.A. 35696584 FBrf0253726
Live imaging of ex-vivo testis with DNA and lysosome markers to explore phagoptosis. The phagocytic cyst cells in Drosophila testis eliminate germ cell progenitors via phagoptosis. Sci. Adv. 35714186 FBrf0253775
We developed a system modeling early neurodegenerative events in Drosophila adult photoreceptor cells. Thanks to the stereotypy of their axonal projections, this system delivers quantitative data on sporadic and progressive axonal degeneration of photoreceptor cells. A Quantitative Model of Sporadic Axonal Degeneration in the Drosophila Visual System. J. Neurosci. 35534228 FBrf0253774

May 2022

Author description of technical advance Title Journal PubMed ID FBrf number
New fluorescent phenotypic markers. Balancer chromosomes for Drosophila simulans. Transgenic tools for targeted chromosome rearrangements allow construction of balancer chromosomes in non-melanogaster Drosophila species. G3 (Bethesda) 35143616 FBrf0253138
The paper offers a computational model that recreates the posterior localization of nanos and polar granule component mRNAs in the oocyte and early embryo. Computational modeling offers new insight into Drosophila germ granule development. Biophys. J. 35288123 FBrf0253258
Measurement of mitochondrial respiratory chain enzymatic activities in D. melanogaster samples. Measurement of mitochondrial respiratory chain enzymatic activities in Drosophila melanogaster samples. STAR Protoc 35479112 FBrf0253336
iPOND identification of replication fork associated proteins in 3-5h embryos and S2 cell lines by quantitative mass spectrometry. Identification of replication fork-associated proteins in Drosophila embryos and cultured cells using iPOND coupled to quantitative mass spectrometry. Sci. Rep. 35484306 FBrf0253333
Our paper describes HyDrop, a completely open-source droplet-microfluidic single-cell sequencing method. HyDrop can work in scRNA-seq or scATAC-seq mode, and has been tested on human, mouse and drosophila samples. Hydrop enables droplet-based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads. eLife 35195064 FBrf0253117
We describe optimized assay for transposase-accessible chromatin by sequencing (ATAC-seq) library preparation using nuclei isolated from adult Drosophila brains. This optimized protocol will facilitate future ATAC-seq studies using adult flies. Optimized assay for transposase-accessible chromatin by sequencing (ATAC-seq) library preparation from adult Drosophila melanogaster neurons. Sci. Rep. 35411004 FBrf0253212
Two new mutant alleles, Yippee[Chi-A] (BL#93858) and Yippee[Delta1] (BL#93859). A fly appeared: sable, a classic Drosophila mutation, maps to Yippee, a gene affecting body color, wings, and bristles. G3 (Bethesda) 35266526 FBrf0253414
Development of a CRISPR/Cas9-based knock-in method to target genes in the Drosophila genome. We also present an updated antennal lobe atlas based on our findings. Chemoreceptor co-expression in Drosophila melanogaster olfactory neurons. eLife 35442190 FBrf0253272
New plasmid and Drosophila lines to overexpress transgenes in Drosophila. A LexAop > UAS > QUAS trimeric plasmid to generate inducible and interconvertible Drosophila overexpression transgenes. Sci. Rep. 35264662 FBrf0252918
Single-cell wounding model, epidermis. Calcium bursts allow rapid reorganization of EFhD2/Swip-1 cross-linked actin networks in epithelial wound closure. Nat. Commun. 35524157 FBrf0253404
Automated, high-resolution quantitative phenotyping of Drosophila intestines based on cell segmentation data. Using cell coordinates, the intestines are computationally linearized and aligned to enable comparative analysis along their whole length. An image analysis method for regionally defined cellular phenotyping of the Drosophila midgut. Cell Rep Methods 35474669 FBrf0253351
The effect of Patronin-RNAi on the microtubule polarity of Class 4 neurons can be assayed using the recombinant line: ppk-gal4, UAS-EB1-TagRFP-T, UAS-Patronin-RNAi (BL36659)/TM6. Microtubule polarity is instructive for many aspects of neuronal polarity. Dev. Biol. 35341730 FBrf0253310
UAS-NCDN (Neurochondrin) transgenic flies. Regulation of the evolutionarily conserved muscle myofibrillar matrix by cell type dependent and independent mechanisms. Nat. Commun. 35562354 FBrf0253445
A new anti-Frl antibody was generated in rat after immunization with a purified recombinant protein containing the amino acid residues 687-1183 of Frl. A Comparative Study of the Role of Formins in Drosophila Embryonic Dorsal Closure. Cells 35563844 FBrf0253495

Apr 2022

Author description of technical advance Title Journal PubMed ID FBrf number
This paper utilizes FIJI macros to quantify cachectic phenotypes such as muscle detachment and lipid droplet size. Analyzing cachectic phenotypes in the muscle and fat body of Drosophila larvae. STAR Protoc 35284841 FBrf0252884
SoAL: tool for social behavior analysis. SDPD-15k: fly social behavior training dataset for SoAL. MIAS: software for video acquisition. Behavioral signatures of structured feature detection during courtship in Drosophila. Curr. Biol. 35139360 FBrf0253010
This paper reports a CRISPR/Cas9 edited genomic mutant of Jra (FBgn0001291) resistant to SUMO conjugation on Lysines 29 and 190. The resultant fly line shows a phenotype consistent with increased activity of Jra. SUMOylation of Jun fine-tunes the Drosophila gut immune response. PLoS Pathog. 35255103 FBrf0252954
We generated new reagents for the field, please refer to the paper for the reagents generated. Derlin-1 and TER94/VCP/p97 are required for intestinal homeostasis. J. Genet. Genomics 34547438 FBrf0253107
6 strains were created or customized for enabling recombination on the 4th chromosome. New resources for the Drosophila 4th chromosome: FRT101F enabled mitotic clones and Bloom syndrome helicase enabled meiotic recombination. G3 (Bethesda) 35084488 FBrf0253111
New resource: measured synaptic surface areas in a variety of neurons in the Drosophila first instar larval central nervous system. Synaptic counts approximate synaptic contact area in Drosophila. PLoS ONE 35377898 FBrf0253082
Tracking of larval locomotion for long periods. Long-Term Observation of Locomotion of Drosophila Larvae Facilitates Feasibility of Food-Choice Assays. Adv Biol (Weinh) 34365739 FBrf0253215
S2R+ cells with stable "LiveDrop" reporters (GFP and mRFP) that marks the surface of lipid droplets. Recruitment of Peroxin 14 to lipid droplets affects lipid storage in Drosophila. J. Cell Sci. 35274690 FBrf0253163
Automated pipeline for quantifying interactions between adjacent glial subsets. Quantifying Glial-Glial Tiling Using Automated Image Analysis in Drosophila. Front. Cell. Neurosci. 35401121 FBrf0253225
Behavioral method for measuring solid food consumption. Identification of additional dye tracers for measuring solid food intake and food preference via consumption-excretion in Drosophila. Sci. Rep. 35418664 FBrf0253152

Mar 2022

Author description of technical advance Title Journal PubMed ID FBrf number
Modified TUNEL protocol to study cell death in tissues. Protocol to study cell death using TUNEL assay in Drosophila imaginal discs. STAR Protoc 35128481 FBrf0252563
We developed a PCR-based NGS protocol to cluster cell lines based on the genome-wide distribution of a limited number of diagnostic TE families. It can accurately identify and authenticate the numerous Drosophila cell lines. A novel transposable element-based authentication protocol for Drosophila cell lines. G3 (Bethesda) 34849844 FBrf0252561
It is improvement on culturing wing imaginal disc and live imaging cytonemes, specially the ones from the Air Sac Primordium. It also contains a follow up Cytoneme Dynamics analysis tool for ImageJ/FIJI and a R/RStudios pipeline for the data analysis and graphical representation. Protocol for ex vivo time lapse imaging of Drosophila melanogaster cytonemes. STAR Protoc 35141564 FBrf0252689
Use of DLM spiking readouts. Distinct Aging-Vulnerable and -Resilient Trajectories of Specific Motor Circuit Functions in Oxidation- and Temperature-Stressed Drosophila. eNeuro 34876473 FBrf0252428
We developed a CRISPR/Cas9-based knockin system (LexA.G4HACK) to replace Gal4 coding sequences with LexA, and a LexAop-based short hairpin RNA expression vector (pWALEXA20) to achieve short hairpin RNA-mediated gene silencing. Transgenic Drosophila lines for LexA-dependent gene and growth regulation. G3 (Bethesda) 35100369 FBrf0252870
A new high-speed imaging method to record ultra-fast photomechanical photoreceptor microsaccades in living flies. High-speed imaging of light-induced photoreceptor microsaccades in compound eyes. Commun. Biol. 35241794 FBrf0252822
NMR-based profiling of polar and non-polar metabolites in dissected larval tissues or whole animals. A toolbox to study metabolic status of Drosophila melanogaster larvae. STAR Protoc 35252884 FBrf0252824
Deep single-cell ATAC-seq dataset of mesoderm / muscle cell fate during embryonic development. Simultaneous cellular and molecular phenotyping of embryonic mutants using single-cell regulatory trajectories. Dev. Cell 35176234 FBrf0252873
We used a new CRISPR Drosophila tafazzin mutant line. This line has the first 889 basepairs removed from the first exon of the tafazzin gene. Additionally, this line has a RFP marker knocked in. NAD supplementation improves mitochondrial performance of cardiolipin mutants. Biochim Biophys Acta Mol Cell Biol Lipids 35051613 FBrf0252704
Real-time optical recording of the formation of a visual memory trace in the ellipsoid body. Differential mechanisms underlie trace and delay conditioning in Drosophila. Nature 35173333 FBrf0252922
Reagents for new spliceform generated. Septins tune lipid kinase activity and PI(4,5)P2 turnover during G-protein-coupled PLC signalling in vivo. Life Sci Alliance 35277468 FBrf0252936
The following are new resources generated in this paper. 1. Rat monoclonal anti-FruM antibody (clone 1C1) 2. Rat monoclonal anti-FruM antibody (clone 1A8) 3. Rat monoclonal anti-FruALL antibody (clone 2E4) 4. Rat monoclonal anti-FruALL antibody (clone 3G11D12). Mutually exclusive expression of sex-specific and non-sex-specific fruitless gene products in the Drosophila central nervous system. Gene Expr. Patterns 35124238 FBrf0252913
High resolution microscopy and ultra-sensitive proteomics of nephrocytes. Scaffold polarity proteins Par3A and Par3B share redundant functions while Par3B acts independent of atypical protein kinase C/Par6 in podocytes to maintain the kidney filtration barrier. Kidney Int. 34929254 FBrf0252977

Feb 2022

Author description of technical advance Title Journal PubMed ID FBrf number
Computational tools for the analysis of loosely-coupled patterns of neuronal activity and for detecting phases in the execution of rhythmic behaviors. Extracting temporal relationships between weakly coupled peptidergic and motoneuronal signaling: Application to Drosophila ecdysis behavior. PLoS Comput. Biol. 34910730 FBrf0252232
Stable Isotope Labelling of Amino Acids in Flies (SILAF) is a cost-effective and highly efficient SILAC technique, adapted to Drosophila laboratory needs. It is based on a holidic food source and achieves 99.5% labelling efficiency with heavy lysine at 15$ per mg of protein. Stable Isotope Labeling of Amino Acids in Flies (SILAF) Reveals Differential Phosphorylation of Mitochondrial Proteins Upon Loss of OXPHOS Subunits. Mol. Cell. Proteomics 33640490 FBrf0252195
New Drosophila transgenic lines generated that can be available at request. Selective autophagy controls innate immune response through a TAK1/TAB2/SH3PX1 axis. Cell Rep. 35081354 FBrf0252505
We have developed allelic drive based transgenic fly that can target the insecticide resistant para 1014F locus. We have also developed a fly line containing 3xP3GFP insertion at para L1014 locus. Reversing insecticide resistance with allelic-drive in Drosophila melanogaster. Nat. Commun. 35022402 FBrf0252383
This paper reports a new direct-drive btl-GFP reporter that can be used to follow tracheal morphology independently of the GAL4/UAS system. A direct-drive GFP reporter for studies of tracheal development in Drosophila. Fly 35094652 FBrf0252525
This manuscript describes the use of micro-computerized tomography (microCT) for measuring the size and morphology of the Drosophila heart. This technique is especially useful for analyzing cardiac hypertrophy in flies. Analysis of Drosophila cardiac hypertrophy by microcomputerized tomography for genetic dissection of heart growth mechanisms. Am J Physiol Heart Circ Physiol 34951542 FBrf0252376
Additions to FlyAtlas 2, Drosophila melanogaster gene expression resource: 1. Profile Search facility, 2. Category Search facility, 3. Additional Tissues, 4. Specialized section on larval midgut pH regions. FlyAtlas 2 in 2022: enhancements to the Drosophila melanogaster expression atlas. Nucleic Acids Res. 34718735 FBrf0252311
A new resource: The mRNA expression (bulk RNA sequencing) of third instar larval ovaries (wild type-Oregon R) through three developmental time points. In addition the mRNA expression of somatic and germ line tissue (separated through Flow sorting) of the ovary in these stages. Distinct gene expression dynamics in germ line and somatic tissue during ovariole morphogenesis in Drosophila melanogaster. G3 (Bethesda) 34849771 FBrf0252584
Python-based code used to quantify object-to-object distances; e.g., mRNA to centrosomes. Drosophila centrocortin is dispensable for centriole duplication but contributes to centrosome separation. G3 (Bethesda) 35100335 FBrf0252569
A versatile toolkit focused on piRNA biology and transposon biology that combines germline transgenic RNAi, GFP marker lines for key proteins of the piRNA pathway. A genetic toolkit for studying transposon control in the Drosophila melanogaster ovary. Genetics 34718559 FBrf0252592
A new method for accessing ovarian maturation by quantifying the amount of yolk with YP1::GFP reporter. Effects of Food and Temperature on Drosophila melanogaster Reproductive Dormancy as Revealed by Quantification of a GFP-Tagged Yolk Protein in the Ovary. Front. Physiol. 35046840 FBrf0252438
Characterization of the role of Naa40 in lipid metabolism in Drosophila, specifically in the larval fat body. Histone acetyltransferase NAA40 modulates acetyl-CoA levels and lipid synthesis. BMC Biol. 35057804 FBrf0252501
Using NanoLuc Binary Technology, we first developed an assay to detect ligand-dependent heterodimerization of the ecdysone receptor (EcR) and retinoid X receptor (RXR) in HEK 293T cells. We also developed HEK293 cells that stably express Ecdysone Importer. Rapid Assessment of Insect Steroid Hormone Entry Into Cultured Cells. Front. Physiol. 35145429 FBrf0252694

Jan 2022

Author description of technical advance Title Journal PubMed ID FBrf number
Development of an automated microinjection system for Drosophila embryos. Multiscale, multi-perspective imaging assisted robotic microinjection of 3D biological structures. Annu Int Conf IEEE Eng Med Biol Soc 34892294 FBrf0252055
We provide two macros to quantify exosome release and autophagy in the Drosophila Neuromuscular junction. Macros to Quantify Exosome Release and Autophagy at the Neuromuscular Junction of Drosophila Melanogaster. Front. Cell Dev. Biol. 34869373 FBrf0252025
The transgenic flies overexpress dEGFR specifically within somatic intestinal stem cells (ISC) and enteroblasts (using the EsgGal4, GFP driver). Membrane therapy using DHA suppresses epidermal growth factor receptor signaling by disrupting nanocluster formation. J. Lipid Res. 33515553 FBrf0252238
Genome sequences for D. suzukii individuals and population genomics analysis. Population genomics of Drosophila suzukii reveal longitudinal population structure and signals of migrations in and out of the continental United States. G3 (Bethesda) 34599814 FBrf0252078
Cell line authentication using transposable element insertions. Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture. Genetics 34849875 FBrf0252038
Utilizing a "lab-in-a-box" mechanism to increase accessibility of research opportunities for undergraduates. Flying in the Face of Adversity: a Drosophila-Based Virtual CURE (Course-Based Undergraduate Research Experience) Provides a Semester-Long Authentic Research Opportunity to the Flipped Classroom. J. Microbiol. Biol. Educ. 34880963 FBrf0252050
Single molecule localization microscopy to visualize SNAP and HALO-tagged endogenous protein in tissue samples. Using the LifeAct peptide for super-resolution imaging of actin organization. A single-molecule localization microscopy method for tissues reveals nonrandom nuclear pore distribution in Drosophila. J. Cell Sci. 34806753 FBrf0252184
GRO-Seq of Stage 5 Drosophila melanogaster embryos is included in the paper. We believe this would be a useful resource for other researchers. Histone variant H2A.Z regulates zygotic genome activation. Nat. Commun. 34853314 FBrf0252039
Using mt-keima, we tried to analyze the incidence of mitophagy in Keyon cells. Mitochondrial aconitase 1 regulates age-related memory impairment via autophagy/mitophagy-mediated neural plasticity in middle-aged flies. Aging Cell 34799973 FBrf0252217
UAS-TM4SF. Fos regulates macrophage infiltration against surrounding tissue resistance by a cortical actin-based mechanism in Drosophila. PLoS Biol. 34990456 FBrf0252327
We utilized the Dorsal-Eye Gal4 (DE-GAL4) to drive the exosome marker GFP-CD63 in the dorsal half of the eye imaginal discs. We detect the GFP-CD63 puncta in the morphogenetic furrow on the ventral side of the eye imaginal discs. Dihydroceramide desaturase promotes the formation of intraluminal vesicles and inhibits autophagy to increase exosome production. iScience 34877496 FBrf0252065
Here we Analyze the integrity of oxidative phosphorylation complexes in Drosophila flight muscles. Analyzing the integrity of oxidative phosphorylation complexes in Drosophila flight muscles. STAR Protoc 34977670 FBrf0252164

2021

Dec 2021

Author description of technical advance Title Journal PubMed ID FBrf number
We developed Bitbow, a highly efficient and easy-to-use multicolor labeling system suitable for neural lineage and morphological studies. Bitbow transgenic lines, with streamlined methods in sample prep, high-resolution imaging and analysis bring unprecedented resolution & scale. Bitbow Enables Highly Efficient Neuronal Lineage Tracing and Morphology Reconstruction in Single Drosophila Brains. Front. Neural Circuits 34744636 FBrf0251755
Optogenetic constructs for light-triggered cyclic AMP production. PACmn for improved optogenetic control of intracellular cAMP. BMC Biol. 34663304 FBrf0251641
Adaptation of FRET-based kinase sensor for AMPK for use in fly. AMPK adapts metabolism to developmental energy requirement during dendrite pruning in Drosophila. Cell Rep. 34788610 FBrf0251912
UAS-human ORF as well as UAS-Drosophila ORF. A cross-species approach for the identification of Drosophila male sterility genes. G3 (Bethesda) 34849808 FBrf0252010
Creation of cell lines with attP cassette at either 25C6 or 99F8 on the 2nd or 3rd chromosomes respectively and the successful RMCE with an associated attB plasmid tool kit. Generation of Drosophila attP containing cell lines using CRISPR-Cas9. G3 (Bethesda) 33963853 FBrf0251996
The paper describes the expression of CS Chrimson and TRPA in motoneurons and how to apply patterned stimulation to evoke activity-dependent synaptic plasticity at the NMJ. A comparison of three different methods of eliciting rapid activity-dependent synaptic plasticity at the Drosophila NMJ. PLoS ONE 34847197 FBrf0251887
New transgenic shRNA to KD oskar mRNA that is substantially more effective during oogenesis that previously available reagents. Knock down analysis reveals critical phases for specific oskar noncoding RNA functions during Drosophila oogenesis. G3 (Bethesda) 34586387 FBrf0252056
Two genes conferring resistance to specific drugs are expressed in opposite sexes by incorporating sex-specific introns disrupting the coding sequences of drug-resistance genes. When the transgenic strain is raised on food supplemented with the corresponding drug, only individuals of the desired sex emerge. A drug-inducible sex-separation technique for insects. Nat. Commun. 32355156 FBrf0245511
CLADES is a technology for cell lineage studies based on CRISPR-Cas9 technology that uses a system of genetic switches to activate and inactivate reporter genes. A programmable sequence of reporters for lineage analysis. Nat. Neurosci. 32719561 FBrf0247972

Nov 2021

Author description of technical advance Title Journal PubMed ID FBrf number
We developed a 3D-printed platform FlyVAB for intravital imaging strategy that enables the visualization of the Drosophila posterior midgut at a single cell level across the ventral abdomen cuticle. Intravital imaging strategy FlyVAB reveals the dependence of Drosophila enteroblast differentiation on the local physiology. Commun. Biol. 34697396 FBrf0251628
An ethoscope extension that allows one to probe arousal threshold using qualitative stimuli. Sensory processing during sleep in Drosophila melanogaster. Nature 34588694 FBrf0251660
Detailed 3C protocol suitable for Drosophila. Investigation of the Basic Steps in the Chromosome Conformation Capture Procedure. Front. Genet. 34616432 FBrf0251540
Metabolic Flux-Balance-Network Models for Drosophila gut microbiome members. Modeling Drosophila gut microbe interactions reveals metabolic interconnectivity. iScience 34712918 FBrf0251721
Model of macrophage infiltration into the inflamed brain, analysis of blood-brain barrier tightness in third instar larval and pupal brains. Brain inflammation triggers macrophage invasion across the blood-brain barrier in Drosophila during pupal stages. Sci. Adv. 34705495 FBrf0251689
We implemented a method to feed flies with stable isotope-labeled methionine and coupled this approach with mass spectrometry analysis to determine the relative activities of different branches of methionine metabolism. A genetic model of methionine restriction extends Drosophila health- and lifespan. Proc. Natl. Acad. Sci. U.S.A. 34588310 FBrf0251481
A method for cryopreserving Drosophila primordial germ cells and reviving original strains from the cryopreserved primordial germ cells has been developed. Offspring production from cryopreserved primordial germ cells in Drosophila. Commun. Biol. 34621004 FBrf0251547
We identified a new allele of O-fut1 mutant and made new transgenes for pen-2 and activated Notch. Identification of a new allele of O-fucosyltransferase 1 involved in Drosophila intestinal stem cell regulation. Biol. Open 34731235 FBrf0251775

Oct 2021

Author description of technical advance Title Journal PubMed ID FBrf number
We designed a new method to quantify shape. Our method is a semi-automatic measurement pipeline that can reliably identify curvatures and landmarks based on manually digitized contours of a 2D anatomical structure. A morphological trait involved in reproductive isolation between Drosophila sister species is sensitive to temperature. Ecol. Evol. 34188829 FBrf0249343
Algorithm to analyse adult behaviours. Drosophila females receive male substrate-borne signals through specific leg neurons during courtship. Curr. Biol. 34174209 FBrf0251042
We used a multivariate analysis of variance to identify relevant SNPs from a genome-wide association study of starvation resistance of DGRP flies after being fed four different diets. This approach yielded a dataset of novel diet-responsive candidate genes. Genome-wide analysis in Drosophila reveals diet-by-gene interactions and uncovers diet-responsive genes. G3 (Bethesda) 34568906 FBrf0251364
Development of an optogenetic system that allows precise spatio-temporal control of Notch signalling using light. Desensitisation of Notch signalling through dynamic adaptation in the nucleus. EMBO J. 34396565 FBrf0251262
This protocol shows how to build a programmed mechanic oscillation system and detailed procedures to conduct sleep deprivation in Drosophila. Protocol for Drosophila sleep deprivation using single-chip board. STAR Protoc 34585161 FBrf0251433
Genome-wide astrocyte gene expression. Circadian regulation of the Drosophila astrocyte transcriptome. PLoS Genet. 34543266 FBrf0251441
Single cell RNA sequencing dataset of the Drosophila brain following acute cocaine consumption. The Drosophila brain on cocaine at single-cell resolution. Genome Res. 34035044 FBrf0251482
Consideration of D. melanogaster as a model insect to map genomic evolution in response to climate change. Eco-genetics of desiccation resistance in Drosophila. Biol. Rev. Camb. Philos. Soc. 33754475 FBrf0251240
Additional dye for tracking food intake and food preference via Con-Ex. Expansion and application of dye tracers for measuring solid food intake and food preference in Drosophila. Sci. Rep. 34625601 FBrf0251557
An explant based time-imaging system for studying olfactory circuit assembly. Cellular bases of olfactory circuit assembly revealed by systematic time-lapse imaging. Cell 34551316 FBrf0251446

Sep 2021

Author description of technical advance Title Journal PubMed ID FBrf number
Novel microscopy approach to measure whole-brain neurodegeneration within the Drosophila brain. A protocol to detect neurodegeneration in Drosophila melanogaster whole-brain mounts using advanced microscopy. STAR Protoc 34382016 FBrf0250121
In this article, we created a two-step approach with the main purpose of helping to assign TF to the regulation of specific genes, using Drosophila melanogaster as a case study. Filtering of Data-Driven Gene Regulatory Networks Using Drosophila melanogaster as a Case Study. Front. Genet. 34394179 FBrf0250139
BiPOLES is a covalently linked version of the anion-channelrhodopsin GtACR2 and cation-channelrhodopsin Chrimson. It allows wavelength-dependent optogenetic silencing (blue light) or activation (red light) of the same neurons. BiPOLES is expressed under 20xUAS control. BiPOLES is an optogenetic tool developed for bidirectional dual-color control of neurons. Nat. Commun. 34312384 FBrf0249792
DNase-seq to identify regulatory regions in two distant Drosophila species (D. melanogaster and D. virilis), assessed evolutionary conservation and adaptive evolution of enhancers throughout multiple stages of embryogenesis to interrogate signs of positive or negative selection. The hourglass model of evolutionary conservation during embryogenesis extends to developmental enhancers with signatures of positive selection. Genome Res. 34266978 FBrf0250943
This study provides a method to combine multiple studies in order to uncover genetic changes not possible to see within typical sample sizes. Identification of conserved transcriptome features between humans and Drosophila in the aging brain utilizing machine learning on combined data from the NIH Sequence Read Archive. PLoS ONE 34379632 FBrf0250159
Quantification of bacteria on the cuticle surface by qPCR. Ratio between Lactobacillus plantarum and Acetobacter pomorum on the surface of Drosophila melanogaster adult flies depends on cuticle melanisation. BMC Res. Notes 34496944 FBrf0251023
Improved light-inducible nuclear export system (iLEXY) - an optogenetic loss-of-function approach that triggers translocation of proteins from the nucleus to the cytoplasm. We present two versions of the system with fast or slow recovery nuclear kinetics for targeted proteins. Extremely rapid and reversible optogenetic perturbation of nuclear proteins in living embryos. Dev. Cell 34363757 FBrf0250332
A novel method for interaction detection to compare the contact dynamics of macrophages in the Drosophila embryo. A framework called macrosight, which analyses the movement and interaction of migrating macrophages, including a segmentation and tracking algorithm. Comparative Study of Contact Repulsion in Control and Mutant Macrophages Using a Novel Interaction Detection. J Imaging 34460738 FBrf0250323
Guinea pig anti-Neuropeptide F (NPF) antibody. The sugar-responsive enteroendocrine neuropeptide F regulates lipid metabolism through glucagon-like and insulin-like hormones in Drosophila melanogaster. Nat. Commun. 34376687 FBrf0250203
NaNuTrap accelerates nuclear labelling in embryos by eliminating the lag associated with GFP maturation (when coupled with maternally deposited GFP). It also converts cytoplasmic GFP expressed in transgenic fly lines into a nuclear label. Works with the existing Gal4/UAS system. NaNuTrap: a technique for in vivo cell nucleus labelling using nanobodies. Development 34328170 FBrf0250933

Aug 2021

Author description of technical advance Title Journal PubMed ID FBrf number
This study describes how to use the SunTag system to image mRNA translation at single mRNA resolution in fixed and live embryos. Dynamics of hunchback translation in real-time and at single-mRNA resolution in the Drosophila embryo. Development 34308974 FBrf0249555
Quantitative proteomic profile of both fat body (third instar larva) and thoracic muscles (pharate adults) were generated here. Both wild type and Dp-depleted tissues were profiled by tandem-mass tag-mass spectrometry (TMT-MS). E2F/Dp inactivation in fat body cells triggers systemic metabolic changes. eLife 34251339 FBrf0249520
Analysis software for live imaging of transcription in early embryos, and MATLAB machine learning analysis pipeline for modeling of Pol II pausing topology using live imaging data. Quantitative imaging of transcription in living Drosophila embryos reveals the impact of core promoter motifs on promoter state dynamics. Nat. Commun. 34301936 FBrf0249544
The use of Voronoi diagrams to quantify the disorganization of a tissue (circumferential actin fibers of Drosophila's heart in this case). Rabphilin silencing causes dilated cardiomyopathy in a Drosophila model of nephrocyte damage. Sci. Rep. 34315987 FBrf0249633
We show that light-field microscopy can be used for long-term high-speed 3D imaging with very low phototoxicity, which can be used to observe the embryo development at very low cost. DiLFM: an artifact-suppressed and noise-robust light-field microscopy through dictionary learning. Light Sci Appl 34315860 FBrf0249628
Morphological and electrophysiological methods to analyse adult abdominal neuromuscular synapses during ageing. Miniature neurotransmission is required to maintain Drosophila synaptic structures during ageing. Nat. Commun. 34285221 FBrf0249540
AnnoMiner is a flexible tool to annotate and integrate epigenetic as well as transcription factor occupancy data on the genome scale. It contains all high-quality ENCODE chromatin data that can be investigated with AnnoMiner. AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators. Sci. Rep. 34326396 FBrf0249589

Jul 2021

Author description of technical advance Title Journal PubMed ID FBrf number
We have developed new split fluorescent protein (FP) systems. Our split FP tagging approach allows us to study the proximity between and localization of multiple proteins endogenously expressed in essentially any cell type in Drosophila. Cell-type-specific, multicolor labeling of endogenous proteins with split fluorescent protein tags in Drosophila. Proc. Natl. Acad. Sci. U.S.A. 34074768 FBrf0249114
Super resolution microscopy and single molecule localisation in adult Drosophila melanogaster brains. Tracking Single Molecule Dynamics in the Adult Drosophila Brain. eNeuro 33875453 FBrf0249175
Dataset to cross-validate candidate genes with significant transcriptional response to temperature or variant showing non-random association with temperature. Use the dataset to focus on genes reported by several previous similar studies or on genes not previously reported. False and true positives in arthropod thermal adaptation candidate gene lists. Genetica 33963492 FBrf0249313
Live imaging of chromatin in 3rd instar larval muscles. Chromatin marked by H2B-dsRed, nuclear envelope marked by Klar-GFP (driven by muscle driver), and active chromatin marked by mintobody-GFP reactive with H3K9ac. Nuclear volume and nucleolus labeled with Cherry-NLS. Live imaging of chromatin distribution reveals novel principles of nuclear architecture and chromatin compartmentalization. Sci. Adv. 34078602 FBrf0249133
Discovery of novel, non-canonical cold shock domains within Unr and determination of their structures (PDB identifiers: 6Y6M, 6Y6E, 6Y4H, 6Y96). Redefining Unr-interactome (protein and RNA) by RIP-seq and quantitative mass spectrometry (PXD018115, PRJEB37467). Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras. Cell Rep. 32697992 FBrf0248824
Active-zone Ca2+ imaging in defined brain dopamine neurons. Presynaptic inhibition of dopamine neurons controls optimistic bias. eLife 34061730 FBrf0249124
Anti-JHAMT antibody (guinea pig). A population of neurons that produce hugin and express the diuretic hormone 44 receptor gene projects to the corpora allata in Drosophila melanogaster. Dev. Growth Differ. 34021588 FBrf0249406
We combine histone labeling with DNA Oligopaints to distinguish old versus new histones and visualize their inheritance patterns at a single-gene resolution in asymmetrically dividing cells in vivo. Characterization of histone inheritance patterns in the Drosophila female germline. EMBO Rep. 34031963 FBrf0249366
New female-killing strains of Drosophila suzukii based on Tetracycline-off system were generated. A transgenic female killing system for the genetic control of Drosophila suzukii. Sci. Rep. 34155227 FBrf0249400
Method to identify E3 ubiquitinated substrates in vivo. The ubiquitin ligase Ariadne-1 regulates neurotransmitter release via ubiquitination of NSF. J. Biol. Chem. 33581113 FBrf0249438
Multiple OAMB antagonists and one OAMB agonist were identified in this paper. A platform utilizing Drosophila ovulation for nonhormonal contraceptive screening. Proc. Natl. Acad. Sci. U.S.A. 34260376 FBrf0249495
Quantitative computational simulation of apical constrictions during ventral furrow formation. Mechanical feedback and robustness of apical constrictions in Drosophila embryo ventral furrow formation. PLoS Comput. Biol. 34228708 FBrf0249494
Method to inflict blunt force injuries in third-instar larvae. Effects of blunt force injuries in third-instar Drosophila larvae persist through metamorphosis and reduce adult lifespan. MicroPubl Biol 34278243 FBrf0249473
This one-step method generates, for any locus, a conditional knockout allele in Drosophila. The allele carries a bright fluorescent marker for easy screening and an attP landing site for subsequent genetic manipulations. One-step CRISPR-Cas9 protocol for the generation of plug & play conditional knockouts in Drosophila melanogaster. STAR Protoc 34095868 FBrf0249159

Jun 2021

Author description of technical advance Title Journal PubMed ID FBrf number
We developed a software to quantify the heartbeat parameters of intact larvae immobilized in a microfluidic device. Our software automatically detects the heart location in a video, extracts and detrends the heartbeat signal, and measures several heartbeat parameters. Open access tool and microfluidic devices for phenotypic quantification of heart function of intact fruit fly and zebrafish larvae. Comput. Biol. Med. 33774273 FBrf0248933
Super resolution live cell microscopy using super resolution by optical photon reassignment (SoRa). Actin-dependent membrane polarization reveals the mechanical nature of the neuroblast polarity cycle. Cell Rep. 34010656 FBrf0249028
UAS construct - mitochondria outer membrane GFP marker; Deep learning strategy for automatic mitochondria segmentation (https://github.com/fabda/Myofibril_paper) Myofibril and mitochondria morphogenesis are coordinated by a mechanical feedback mechanism in muscle. Nat. Commun. 33828099 FBrf0248612
A new temporal conditioning behavioral paradigm with automated classification of behavior types and quantification of behavioral rhythms. Drosophila acquires seconds-scale rhythmic behavior. J. Exp. Biol. 33795422 FBrf0249000
Development of an intersectional genetic luciferase reporter of dVGLUT expression specifically in dopamine neurons. Vesicular glutamate transporter modulates sex differences in dopamine neuron vulnerability to age-related neurodegeneration. Aging Cell 33909313 FBrf0249030
Live imaging of translation in living drosophila embryos Imaging translation dynamics in live embryos reveals spatial heterogeneities. Science 33927056 FBrf0249049
A new genome targeting technique to generate clean custom alleles that only have the desired mutation(s) is described in this paper. Plasmid vectors have been deposited to the DGRC, and tool flies generated in this study are available upon request. Scarless engineering of the Drosophila genome near any site-specific integration site. Genetics 33772309 FBrf0249020
New injury method to study CNS regeneration in adults A novel injury paradigm in the central nervous system of adult Drosophila: molecular, cellular and functional aspects. Dis. Model Mech. 34061177 FBrf0249170
SunTag method for imaging translation at single mRNA resolution in fixed and live embryos Dynamics of hunchback translation in real-time and at single-mRNA resolution in the Drosophila embryo. Development 33722899 FBrf0249005
We have generated UAS lines for Toll-2, Toll-6 and Toll-8 tagged with fluorescent markers for full-length receptors, receptors deleted of their extracellular domains and receptors deleted of their intracellular domains and made constructs to express Toll-8 in the early embryo. Formation of polarized contractile interfaces by self-organized Toll-8/Cirl GPCR asymmetry. Dev. Cell 33932333 FBrf0249144
A clustering algorithm designed for detecting conserved gene co-clusters among two species Bipartite tight spectral clustering (BiTSC) algorithm for identifying conserved gene co-clusters in two species. Bioinformatics 32814973 FBrf0249225

May 2021

Author description of technical advance Title Journal PubMed ID FBrf number
Quantitative analysis of parkin-dependent mitophagy using confocal microscopy 3D quantification of autophagy activation and autophagosome-to-mitochondria recruitment in a Drosophila model of Parkinson's disease. STAR Protoc 33851139 FBrf0248763
Seahorse experiments on cardiac tissue Fat-body brummer lipase determines survival and cardiac function during starvation in Drosophila melanogaster. iScience 33889813 FBrf0248791
Development of proteomics of protein trafficking Proteomics of protein trafficking by in vivo tissue-specific labeling. Nat. Commun. 33888706 FBrf0248752
Antibodies generated for AIF and DNase II DNase II mediates a parthanatos-like developmental cell death pathway in Drosophila primordial germ cells. Nat. Commun. 33863891 FBrf0248742
A novel Drosophila model for mild traumatic brain injury for investigation of lifelong brain deficits and degeneration, it also has a new imaging-based approach for analyzing brain pathology in whole mount brains. Repetitive mild head trauma induces activity mediated lifelong brain deficits in a novel Drosophila model. Sci. Rep. 33958652 FBrf0248899
We generated a roGFP-CAAX construct (for mammalian expression) that can be used to examine the redox-state on the plasma membrane. Dihydroceramide desaturase regulates the compartmentalization of Rac1 for neuronal oxidative stress. Cell Rep. 33852856 FBrf0248757
A fluorogen activating protein neuropeptide (Dilp2-FAP) construct was used with membrane impermeant malachite green derivatives (MG-TCarb and MG-B-Tau) to detect neuropeptide release in the brain, specifically in LNv clock neurons Temporally and spatially partitioned neuropeptide release from individual clock neurons. Proc. Natl. Acad. Sci. U.S.A. 33875606 FBrf0248728
Here we design a microfluidic device capable of ensuring the normal development of multiple fly embryos as well as achieving real-time temperature control and fast temperature switches for quantitative live imaging with a home-built two-photon microscope. Quantifying Temperature Compensation of Bicoid Gradients with a Fast T-Tunable Microfluidic Device. Biophys. J. 32853562 FBrf0248966
We use whole-genome sequencing of Drosophila tissues (gut, head) to discover somatic genetic variation: 1- short-read Illumina sequencing of low-input DNA isolated from spontaneous clonal gut neoplasia, 2- long-read Oxford Nanopore (ONT) sequencing of DNA from pooled tissues. Unraveling the features of somatic transposition in the Drosophila intestine. EMBO J. 33634906 FBrf0248816
The work uses the isotropic fractionator method with Drosophila and mosquito brains. This method allows counting the number of cells in a tissue. If can be used with an antibody or genetic labeling (GAL4/UAS or QF/QUAS) and be applied to counting sub-populations of a tissue. The number of neurons in Drosophila and mosquito brains. PLoS ONE 33989293 FBrf0248958
GRAF plays a role in restricting the constriction of the actomyosin based contractile ring in cellularization. Spatiotemporal recruitment of RhoGTPase protein GRAF inhibits actomyosin ring constriction in Drosophila cellularization. eLife 33835025 FBrf0248856

Apr 2021

Author description of technical advance Title Journal PubMed ID FBrf number
We have developed an automated imaging system constituted of a light sheet fluorescence microscope on a chip that allows analysis of Drosophila embryos in suspension that are fluxing in through a microfluidic chamber. Automatic imaging of Drosophila embryos with light sheet fluorescence microscopy on chip. J. Biophotonics 33295053 FBrf0248287
Method to quantify epithelial barrier permeability in Drosophila imaginal discs using fluorescent dextran. The permeability of the experimental sample is compared to control samples that have a disrupted or non-functional barrier. Modified from Lamb et al. (1998). Ecdysone regulates the Drosophila imaginal disc epithelial barrier, determining the length of regeneration checkpoint delay. Development 33658221 FBrf0248455
We developed PEGASUS_flies, which calculates whole gene significance scores from variant P-values that were output in a GWAS. Our platform works well for Drosophila/Drosophila Genetic Reference Panel (DGRP) lines. Available at: https://github.com/ramachandran-lab/PEGASUS_flies Natural variation in the regulation of neurodevelopmental genes modifies flight performance in Drosophila. PLoS Genet. 33735180 FBrf0248437
Hypoxia chamber with strictly controlled environmental parameters Posthypoxic behavioral impairment and mortality of Drosophila melanogaster are associated with high temperatures, enhanced predeath activity and oxidative stress. Exp. Mol. Med. 33564101 FBrf0248297
We introduced DrosoX technique (Scitech Korea, Republic of Korea) for the quantitative analysis of food intake by individual flies. Cucurbitacin B Suppresses Hyperglycemia Associated with a High Sugar Diet and Promotes Sleep in Drosophila melanogaster. Mol. Cells 33542166 FBrf0248331
The "resource" is an accurate phylogeny for the montium group of Drosophila A phylogeny for the Drosophila montium species group: A model clade for comparative analyses. Molec. Phylog. Evol. 33387647 FBrf0248412
UAS-based transgenic lines for expressing genes from the SARS-CoV-2 virus that causes COVID-19 were generated. Functional analysis of SARS-CoV-2 proteins in Drosophila identifies Orf6-induced pathogenic effects with Selinexor as an effective treatment. Cell Biosci. 33766136 FBrf0248509
Targated DamID of olfactory sensory neuron populations Targeted molecular profiling of rare olfactory sensory neurons identifies fate, wiring, and functional determinants. eLife 33666172 FBrf0248540
pPWG-attB empty vector. A modified pPWG vector bearing the attB region inserted at a StuI site. It is compatible with Gateway system and can be used for random insertion in the genome (as a standard pPWG) but also in attB/P site specific integration ( phiC31 mediated). Mauve/LYST limits fusion of lysosome-related organelles and promotes centrosomal recruitment of microtubule nucleating proteins. Dev. Cell 33725482 FBrf0248552
Identification of mRNA targets of Ataxin2 (Atx2) in Drosophila brain by fusing it to the catalytic domain of adenosine deaminase (ADAR) enzyme. ADAR converts adenosine into inosine and subsequent RNA-Seq identifies these conversions (edits) as guanosines. Antagonistic roles for Ataxin-2 structured and disordered domains in RNP condensation. eLife 33689682 FBrf0248408
Single molecule fluorescence in situ hybridisation in whole Drosophila brain. Selective dendritic localization of mRNA in Drosophila mushroom body output neurons. eLife 33724180 FBrf0248505
Novel method to compare 3D chromatin conformation data in Drosophila Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning. Nat. Genet. 33795866 FBrf0248615
A lineage recording system termed "intMEMOIR" designed for in situ readout, thereby enabling simultaneous analysis of cell lineage, state, and spatial organization in the same tissue. Imaging cell lineage with a synthetic digital recording system. Science 33833095 FBrf0248662

Mar 2021

Author description of technical advance Title Journal PubMed ID FBrf number
We describe a fluorescent in situ hybridization protocol for the detection of endogenous Drosophila gut microbiome bacteria in different sample types (isolated bacteria, feces, larval and adult guts). We also added an automated analysis pipeline, which should be useful for others. Visualization of endogenous gut bacteria in Drosophila melanogaster using fluorescence in situ hybridization. PLoS ONE 33606846 FBrf0248171
FreeClimber is an automated and high-throughput method for accurately and repeatably quantifying group climbing performance/climbing velocity/negative geotaxis in Drosophila. For more information, see the GitHub repository at: https://github.com/adamspierer/freeclimber FreeClimber: automated quantification of climbing performance in Drosophila. J. Exp. Biol. 33188065 FBrf0247781
CLADES, a tool to analyze neuronal lineages in Drosophila. A programmable sequence of reporters for lineage analysis. Nat. Neurosci. 32719561 FBrf0247972
The paper describes the use of Hedgehog signaling compenents: The signal Hedgehog and receptor Patched directed expression to model mutually exclusive computations in the context and highlights useful applications and tries to imagine the technology's potential. A Turing machine for the Life Sciences. D. I. S. FBrf0248044
New antibody, new transgenic lines, new S2 cell stable cell lines. Drosophila Tubulin-Specific Chaperone E Recruits Tubulin around Chromatin to Promote Mitotic Spindle Assembly. Curr. Biol. 33259793 FBrf0248211
In this manuscript it is reported a new setup to evaluate for the first time the release of neuroactive amines in Drosophila brain, by in vivo Fast-Scan Cyclic Voltammetry, while the fly is being exposed to odorants or an electric shock. Study of the release of endogenous amines in Drosophila brain in vivo in response to stimuli linked to aversive olfactory conditioning. J. Neurochem. 32596813 FBrf0248195
Generation of novel transgenic flies expressing a monocistronic version of the human FUS gene (expresses only the FUS protein or only the altFUS protein), as well as the wild-type human FUS gene (expresses both proteins, FUS and altFUS). The FUS gene is dual-coding with both proteins contributing to FUS-mediated toxicity. EMBO Rep. 33226175 FBrf0248130
Gene Drive element (split) located in specific Drosophila melanogaster genes. Inherently confinable split-drive systems in Drosophila. Nat. Commun. 33674604 FBrf0248266
By using the previously defined matrisomes of Drosophila, we analyzed recorded genotype-to-phenotype relationships to define the Drosophila extracellular matrix phenome. The extracellular matrix phenome across species. Matrix Biol Plus 33543035 FBrf0247970
This article indicates the maximum length of introgession segments that produce hybrid segmental offspring in heterozygosity, introgressing chromosomal segments of D. koepferae into a genetic background of D. buzzatii. Evaluation of Drosophila chromosomal segments proposed by means of simulations of possessing hybrid sterility genes from reproductive isolation. J. Genet. 33622987 FBrf0248240

Feb 2021

Author description of technical advance Title Journal PubMed ID FBrf number
This paper describes reagents (e.g. transgenic flies, plasmids, cloning protocols) to perform prime editing in Drosophila melanogaster. Precise genome engineering in Drosophila using prime editing. Proc. Natl. Acad. Sci. U.S.A. 33443210 FBrf0247772
Metabolic flux analysis of lipids. Lipidome-wide 13C flux analysis: a novel tool to estimate the turnover of lipids in organisms and cultures. J. Lipid Res. 31712250 FBrf0247854
Developmental scRNA-seq atlas of the Drosophila optic lobe. Neuronal diversity and convergence in a visual system developmental atlas. Nature 33149298 FBrf0247762
Application of digital droplet PCR in gene expression study. Genes regulating development and behavior exhibited altered expression in Drosophila melanogaster exposed to bisphenol A: use of real-time quantitative PCR (qRT-PCR) and droplet digital PCR (ddPCR) in genotoxicity study. Environ. Sci. Pollut. Res. Int. 33025430 FBrf0247932
The transgenic sexing strains of Drosophila suzukii based on the testis-specific fluorescent expression. Characterization of the Drosophila suzukii β2-tubulin gene and the utilization of its promoter to monitor sex separation and insemination. Gene 33346099 FBrf0247834
New model of flight exercise, new model of the Western Diet. Preference and detrimental effects of high fat, sugar, and salt diet in wild-caught Drosophila simulans are reversed by flight exercise. FASEB Bioadv 33490883 FBrf0247838
Identification of neutral lipid-based secreted structures called microcarriers in the lumen of the male accessory gland, which can be stained by neutral lipid dyes like LipidTox and Nile Red. Drosophila Sex Peptide controls the assembly of lipid microcarriers in seminal fluid. Proc. Natl. Acad. Sci. U.S.A. 33495334 FBrf0247869
Long-term in vivo imaging of Drosophila giant larvae tumor migration and invasion using SiMView microscopy. The level of oncogenic Ras determines the malignant transformation of Lkb1 mutant tissue in vivo. Commun. Biol. 33514834 FBrf0247944
Methods to examine the musculature of the Drosophila larva. These methods include analysis of the muscle sarcomeres, particularly in the same larva throughout the different larval instars. This work contains methods to muscle structural changes to muscle functional changes. Analyzing muscle structure and function throughout the larval instars in live Drosophila. STAR Protoc 33532738 FBrf0247996
We verified that Drosophila S2R+ adapted to grow in serum-free media is amenable to RNAi interference-mediated gene knockdown. Serum-free adapted Drosophila S2R+ line is amenable to RNA interference. Micropub Biol 33537561 FBrf0248021
Single cell genomics of testes. Dynamic sex chromosome expression in Drosophila male germ cells. Nat. Commun. 33563972 FBrf0248088
New reporter line and new null allele were generated in this paper. The Krüppel-like factor Cabut has cell cycle regulatory properties similar to E2F1. Proc. Natl. Acad. Sci. U.S.A. 33558234 FBrf0248123
Split-GAL4 lines labeling specific cell types. Neural circuit mechanisms of sexual receptivity in Drosophila females. Nature 33239786 FBrf0247919
A translational fidelity reporter (UAS-Fluc-STOP-Nluc) - Drosophila mutant strains (RPS23-R67K, RPS26-KO). Ribosomopathy-associated mutations cause proteotoxic stress that is alleviated by TOR inhibition. Nat. Cell Biol. 33495632 FBrf0248082
The modified PER assay can deliver stimuli not only for taste, but also for other senses. We made a line that can express the hair plate in legs. Multisensory interactions regulate feeding behavior in Drosophila. Proc. Natl. Acad. Sci. U.S.A. 33558226 FBrf0248109
UAS-MagIC, fluorescent Mg2+ reporter transgene. Magnesium efflux from Drosophila Kenyon cells is critical for normal and diet-enhanced long-term memory. eLife 33242000 FBrf0247921
Mathematical algorithm for cytoneme/Tumor microtube expansion. Modeling invasion patterns in the glioblastoma battlefield. PLoS Comput. Biol. 33513131 FBrf0248065
We developed a new technique called mosaic analysis by gRNA-induced crossing-over (MAGIC) for mosaic analysis with unmodified genomes. We developed the MAGIC toolkit for chromosomal arm 2L. Versatile CRISPR/Cas9-mediated mosaic analysis by gRNA-induced crossing-over for unmodified genomes. PLoS Biol. 33444322 FBrf0247818

Jan 2021

Author description of technical advance Title Journal PubMed ID FBrf number
Human genes expressed in breast cancer patients are screened for their ability to aberrate development of the Drosophila eye. Transgenic construct UAS-hRPS12 was described in this paper. HumanaFly: high-throughput transgenesis and expression of breast cancer transcripts in Drosophila eye discovers the RPS12-Wingless signaling axis. Sci. Rep. 33273532 FBrf0247452
Python-based code used to quantify object-to-object distances; e.g., mRNA to centrosomes. centrocortin RNA localization to centrosomes is regulated by FMRP and facilitates error-free mitosis. J. Cell Biol. 33196763 FBrf0247305
A single cell atlas of the proximal wing disc was built by single cell RNAseq. The myoblast, tracheal and epithelial cells associated with third instar larval wing disc were mapped. Diverse cell types along with specific markers were identified. A cell atlas of adult muscle precursors uncovers early events in fibre-type divergence in Drosophila. EMBO Rep. 32815271 FBrf0247435
Expansion microscopy for larval tissue. Recruitment of BAF to the nuclear envelope couples the LINC complex to endoreplication. Development 33168584 FBrf0247504
Several new fly lines. In particular: - a GFP-tagged FoxP gene - a null allele - a conditional UAS-gRNA-based knock-out line. Identification of FoxP circuits involved in locomotion and object fixation in Drosophila. Open Biol 33321059 FBrf0247550
Nuclear localization signal (NLS) that isolated from D. suzukii transformer gene. Bicistronic expression and differential localization of proteins in insect cells and Drosophila suzukii using picornaviral 2A peptides. Insect Biochem. Mol. Biol. 31978587 FBrf0245063
piggyBac constructs that express DeRed at embryonic stage. Identification and characterization of four Drosophila suzukii cellularization genes and their promoters. BMC Genet. 33339500 FBrf0247583
The protocol describes preparation of adult axenic Drosophila before monitoring their behavior in a two-choice feeding assay, where flies are confronted with an axenic versus a dead or alive bacteria-contaminated feeding solution. Protocol for a Binary Choice Feeding Assay Using Adult, Axenic Drosophila. STAR Protoc 33377013 FBrf0247622
CRISPR dual-gRNA transgenic targeting phosphoinositide signaling genes. A genome engineering resource to uncover principles of cellular organization and tissue architecture by lipid signaling. eLife 33320085 FBrf0247664
Tissue- and time-resolved chromatin accessibility during Drosophila embryogenesis. Lineage-Resolved Enhancer and Promoter Usage during a Time Course of Embryogenesis. Dev. Cell 33171098 FBrf0247494
We apply deep learning on thousands of mRNA datasets to examine the genetic regulatory code controlling mRNA abundance in model organisms including Drosophila melanogaster, and show that in all organisms mRNA abundance can be predicted directly from DNA sequence. Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure. Nat. Commun. 33262328 FBrf0247517
UAS-driven regulatable fluorescent secretory cargo.] ESCargo: a regulatable fluorescent secretory cargo for diverse model organisms. Mol. Biol. Cell 33112725 FBrf0247546
1. S2 cell culture and luciferase reporter assay; 2. AGO1 immunoprecipitation (AGO1 IP); 3. Immunofluorescence experiments. Regulatory mechanism of daily sleep by miR-276a. FASEB J. 33337563 FBrf0247672
Resource: website for downloading aligned genome sequences from Drosophila pseudoobscura species group. PseudoBase: a genomic visualization and exploration resource for the Drosophila pseudoobscura subgroup. Fly 33319644 FBrf0247745
S2 cell culture and luciferase reporter assay; AGO1 immunoprecipitation. Regulation of circadian behavioural output via clock-responsive miR-276b. Insect Mol. Biol. 33131172 FBrf0247752
Superresolution imaging of glutamate receptors were obtained with structured illumination microscopy (SIM). Postsynaptic cAMP signalling regulates the antagonistic balance of Drosophila glutamate receptor subtypes. Development 33234716 FBrf0247665
Characterization of novel chromosomal structures in Drosophila embryonic cells, by combining 3D structured illumination microscopy (3D-SIM) and DAPI or FISH staining with a X Oligopaint probe (observation in a haploid context in sorted male embryos using a Y-GFP line). Ext. Fig.6. Regulation of single-cell genome organization into TADs and chromatin nanodomains. Nat. Genet. 33077913 FBrf0247675
The methods paper describes detailed procedure for X-ray fluorescence microscopy scanning of Drosophila oocytes and eggs to measure elemental distribution. Our report on the elemental distributions themselves was published in Hu et al. iScience 2020. X-ray fluorescence microscopy scanning of Drosophila oocytes and eggs. STAR Protoc 33437967 FBrf0247770

2020

Dec 2020

Author description of technical advance Title Journal PubMed ID FBrf number
Analysis of Gal4 expression patterns of commonly used Gal4 drivers in adult females. Analysis of Gal4 Expression Patterns in Adult Drosophila Females. G3 (Bethesda) 32917721 FBrf0247159
We defined the origins of repeat-derived RNAs and their specific chromatin locations in Drosophila S2 cells using the global RNA–DNA interaction sequencing method (GRID-seq). Active retrotransposons help maintain pericentromeric heterochromatin required for faithful cell division. Genome Res. 33060173 FBrf0247182
We have developed a novel automated Drosophila life cycle multi-phase transition (pupariation, eclosion, and death) timing detection and measurement system with high accuracy and high temporal resolution. The Drosophila Individual Activity Monitoring and Detection System (DIAMonDS). eLife 33168136 FBrf0247192
A hydrogen peroxide probe was detected in vivo through a burnt fluorescent probe (TCFB, 2-Dicyanomethylene-3-cyano-4,5,5-trimethyl-2,5-dihydrofuran) (Sedgwick et al., 2017). Intramacrophage ROS Primes the Innate Immune System via JAK/STAT and Toll Activation. Cell Rep. 33176146 FBrf0247218
The binary expression of different pro-apoptotic genes using 2A peptides. Functional characterization of the Drosophila suzukii pro-apoptotic genes reaper, head involution defective and grim. Apoptosis 33113043 FBrf0247316
Improved pipeline for CRISPR mediated genome editing in Drosophila species. Generation of new vector to make donor plasmids for homology-directed repair. A pipeline for precise and efficient genome editing by sgRNA-Cas9 RNPs in Drosophila. Fly 33016195 FBrf0247326
We describe a novel high throughput mass spectrometry approach to identifying species and sex by their metabolites. We show it works invertebrates generally, and can accurately distinguish closely related Drosophila (e.g. melanogaster and simulans) with potential for mass scoring. The application of rapid evaporative ionization mass spectrometry in the analysis of Drosophila species-a potential new tool in entomology. Open Biol. 33234068 FBrf0247327
Here we introduce TEchim, a new software that extracts chimeric sequencing reads that span transposon-gene breakpoints. In addition, we introduce scHardyWeinberg, a new approach to quantify co-expression levels in high-throughput single-cell sequencing data. Transposon expression in the Drosophila brain is driven by neighboring genes and diversifies the neural transcriptome. Genome Res. 32973040 FBrf0247119
Single-cell RNA-sequencing dataset of the adult Drosophila ovary containing transcriptome profiles for all major ovarian cell types. A single-cell atlas and lineage analysis of the adult Drosophila ovary. Nat. Commun. 33159074 FBrf0247148
We developed an optimized version of the bright and fast-maturing fluorescent protein mNeonGreen to serve as a real-time, quantitative reporter of gene/enhancer expression. A sensitive mNeonGreen reporter system to measure transcriptional dynamics in Drosophila development. Commun. Biol. 33184447 FBrf0247254
DRB treatment followed by Pol II ChIP. Evidence of slightly increased Pol II pausing in UPF1-depleted Drosophila melanogaster cells. Micropub Biol 33274326 FBrf0247413

Nov 2020

Author description of technical advance Title Journal PubMed ID FBrf number
Antibody. AANAT1 functions in astrocytes to regulate sleep homeostasis. eLife 32955431 FBrf0246918
Endogenous locus was edited with a two-step CRISPR/Cas9-mediated replacement. Humanization of Drosophila Gαo to Model GNAO1 Paediatric Encephalopathies. Biomedicines 33036271 FBrf0246897
We optimized, tested, and introduced a new method of automated count of Drosophila adults using the SeedCounter mobile application. The application is available on all mobile devices based on the Android system, and it does not require any additional equipment. Quantifying Drosophila adults with the use of a smartphone. Biol. Open 32917765 FBrf0246907
We introduce a developmental 96-well plate assay to use individual Drosophila larvae as tool for metabolic studies. How to use the development of individual Drosophila larvae as a metabolic sensor. J. Insect Physiol. 32783958 FBrf0246919
Novel method to compare 3D chromatin conformation data in Drosophila. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nat. Genet. 33077914 FBrf0247073
Comprehensive calcium imaging from all 2,000 Kenyon cells in the mushroom body at single cell resolution. Synthesis of Conserved Odor Object Representations in a Random, Divergent-Convergent Network. Neuron 32814018 FBrf0247109
Dominant negative form of IP3R protein. It has three mutated amino acids which prevent ligand binding. IP3R being tetramer, requires IP3 binding to all monomers. Hence presence of even single IP3R-DN monomer in tetramer can render whole IP3R protein complex functionless. Modulation of flight and feeding behaviours requires presynaptic IP3Rs in dopaminergic neurons. eLife 33155978 FBrf0247160
Use of Hydrogel for live-imaging of Drosophila ovaries. Collective Cell Sorting Requires Contractile Cortical Waves in Germline Cells. Curr. Biol. 32916115 FBrf0247169
This paper uses fast-scan cyclic voltammetry at a carbon-fiber microelectrode to make real-time measurement of stimulated endogenous dopamine release in the mushroom body of adult Drosophila brains using various stimulation techniques. Real-Time Measurement of Stimulated Dopamine Release in Compartments of the Adult Drosophila melanogaster Mushroom Body. Anal. Chem. 33048531 FBrf0247175
New measurements of Position weight Matrices (PWMs) Dinucleotide Position weight Matrices (DPWMs) for 13 Drosophila transcription factors and their DNA shape analysis for all shape features. Transcription Factor Binding Affinities and DNA Shape Readout. iScience 33163946 FBrf0247184
Sequence, features, and schematic of the pWattB-nlacZ reporter construct vector. Three distinct mechanisms, Notch instructive, permissive, and independent, regulate the expression of two different pericardial genes to specify cardiac cell subtypes. PLoS ONE. 33108408 FBrf0247019
A new method for immobilizing explanted Drosophila tissue in agarose for use in long-term live imaging. An Immobilization Technique for Long-Term Time-Lapse Imaging of Explanted Drosophila Tissues. Front. Cell Dev. Biol. 33117817 FBrf0247101
Using new fast-scan cyclic voltammetry serotonin specific waveforms for in vivo detection of serotonin in Drosophila tissue. Improving serotonin fast-scan cyclic voltammetry detection: new waveforms to reduce electrode fouling. Analyst 32955048 FBrf0247149
We have developed a new protocol to indcue cell cycle arrest in early embryos, and deposited RNA-seq data for WT embryos and embryos arrested in cycle 12 for differernt amount of time. Interphase-arrested Drosophila embryos activate zygotic gene expression and initiate mid-blastula transition events at a low nuclear-cytoplasmic ratio. PLoS Biol. 33090988 FBrf0247179
Analysis of the chronometabolome including lipids. Loss of function in the Drosophila clock gene period results in altered intermediary lipid metabolism and increased susceptibility to starvation. Cell. Molec. Life Sci. 31960114 FBrf0247228
Transgenic Targeted DamID construct for the gene polycomb-like (Pcl) under the control of a UAS. Persistent epigenetic reprogramming of sweet taste by diet. Sci. Adv. 33177090 FBrf0247230

Oct 2020

Author description of technical advance Title Journal PubMed ID FBrf number
Small molecules called "HACs" alter normal autoprocessing activity of hedgehog precursor protein. Instead of reacting with cholesterol (cholesterolysis), the HACs alter hedgehog precursor autoprocessing toward a side reaction with water (hydrolysis). Subverting Hedgehog Protein Autoprocessing by Chemical Induction of Paracatalysis. Biochemistry 32013401 FBrf0246799
This paper shows how computational network analyses based on protein-protein interactions can be used to augment genetic screens to identify genes involved in essential developmental processes. The code are deposited in GitHub https://github.com/extavourlab/hpo_ova_eggL_screen. Topology-driven protein-protein interaction network analysis detects genetic sub-networks regulating reproductive capacity. eLife 32901612 FBrf0246922
PhotoGal4 is a phytochrome B-based optogenetic switch for fine tuned spatiotemporal control of gene expression in Drosophila explants. PhotoGal4 activates and deactivates gene expression upon red- or far-red-light irradiation. PhotoGal4: A Versatile Light-Dependent Switch for Spatiotemporal Control of Gene Expression in Drosophila Explants. iScience 32652492 FBrf0246250
We developed a unique visual stimulation setup to probe spectral, spatial, & temporal properties using neural activity imaging. Custom optical filters enabled simultaneous two-photon imaging & visual stimulation over a wide range of hues without compromising the temporal rates. A novel setup for simultaneous two-photon functional imaging and precise spectral and spatial visual stimulation in Drosophila. Sci. Rep. 32973185 FBrf0246808
New white gene mutant strains were generated in Drosophila suzukii and can be used as resources to study the corresponding phenotype. CRISPR/Cas9 mediated disruption of the white gene leads to pigmentation deficiency and copulation failure in Drosophila suzukii. J. Insect Physiol. 32745561 FBrf0246889
This protocol allows generation of homozygous mutant cell lines using an insertion cassette which autocatalytically generates insertion mutations in all alleles. Knockout cells generated using this method can be directly identified by PCR without a need for DNA sequencing. CRISPR-based engineering of gene knockout cells by homology-directed insertion in polyploid Drosophila S2R+ cells. Nat. Protoc. 32958931 FBrf0246845
Drosophila melanogaster line infected only with galbut virus (FoCo-17 line 30). Partitiviruses Infecting Drosophila melanogaster and Aedes aegypti Exhibit Efficient Biparental Vertical Transmission. J. Virol. 32759315 FBrf0246864
The isobaric tags for relative and absolute quantification (iTRAQ) technology was chosen to sequence the proteomes of Drosophila. Comparative proteomics analysis of dietary restriction in Drosophila. PLoS ONE 33064752 FBrf0246967