FlyBase:Papers with technical advances

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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

2021

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. [https://pubmed.ncbi.nlm.nih.gov/33443210/ 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

FBrf number PubMed ID Journal Title Author description of technical advance
FBrf0247452 33273532 Sci. Rep. HumanaFly: high-throughput transgenesis and expression of breast cancer transcripts in Drosophila eye discovers the RPS12-Wingless signaling axis. 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.
FBrf0247305 33196763 J. Cell Biol. centrocortin RNA localization to centrosomes is regulated by FMRP and facilitates error-free mitosis. Python-based code used to quantify object-to-object distances; e.g., mRNA to centrosomes
FBrf0247435 32815271 EMBO Rep. A cell atlas of adult muscle precursors uncovers early events in fibre-type divergence in Drosophila. 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.
FBrf0247504 33168584 Development Recruitment of BAF to the nuclear envelope couples the LINC complex to endoreplication. Expansion microscopy for larval tissue
FBrf0247550 33321059 Open Biol. Identification of FoxP circuits involved in locomotion and object fixation in Drosophila. Several new fly lines. In particular: - a GFP-tagged FoxP gene - a null allele - a conditional UAS-gRNA-based knock-out line.
FBrf0245063 31978587 Insect Biochem. Mol. Biol. Bicistronic expression and differential localization of proteins in insect cells and Drosophila suzukii using picornaviral 2A peptides. nuclear localization signal (NLS) that isolated from D. suzukii transformer gene
FBrf0247583 33339500 BMC Genet. Identification and characterization of four Drosophila suzukii cellularization genes and their promoters. piggyBac constructs that express DeRed at embryonic stage
FBrf0247622 33377013 STAR Protoc Protocol for a Binary Choice Feeding Assay Using Adult, Axenic Drosophila. 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.
FBrf0247664 33320085 eLife A genome engineering resource to uncover principles of cellular organization and tissue architecture by lipid signaling. CRISPR dual-gRNA transgenic targeting phosphoinositide signaling genes
FBrf0247494 33171098 Dev. Cell Lineage-Resolved Enhancer and Promoter Usage during a Time Course of Embryogenesis. Tissue- and time-resolved chromatin accessibility during Drosophila embryogenesis
FBrf0247517 33262328 Nat. Commun. Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure. 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.
FBrf0247546 33112725 Mol. Biol. Cell ESCargo: a regulatable fluorescent secretory cargo for diverse model organisms. UAS-driven regulatable fluorescent secretory cargo
FBrf0247672 33337563 FASEB J. Regulatory mechanism of daily sleep by miR-276a. 1. S2 cell culture and luciferase reporter assay; 2. AGO1 immunoprecipitation (AGO1 IP); 3. Immunofluorescence experiments;
FBrf0247745 33319644 Fly PseudoBase: a genomic visualization and exploration resource for the Drosophila pseudoobscura subgroup. Resource: website for downloading aligned genome sequences from Drosophila pseudoobscura species group
FBrf0247752 33131172 Insect Mol. Biol. Regulation of circadian behavioural output via clock-responsive miR-276b. S2 cell culture and luciferase reporter assay; AGO1 immunoprecipitation
FBrf0247665 33234716 Development Postsynaptic cAMP signalling regulates the antagonistic balance of Drosophila glutamate receptor subtypes. superresolution imaging of glutamate receptors were obtained with structured illumination microscopy (SIM)
FBrf0247675 33077913 Nat. Genet. Regulation of single-cell genome organization into TADs and chromatin nanodomains. 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
FBrf0247770 33437967 STAR Protoc X-ray fluorescence microscopy scanning of Drosophila oocytes and eggs. 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.

2020

Dec 2020

FBrf number PubMed ID Journal Title Author description of technical advance
FBrf0247159 32917721 G3 (Bethesda) Analysis of Gal4 Expression Patterns in Adult Drosophila Females. Analysis of Gal4 expression patterns of commonly used Gal4 drivers in adult females.
FBrf0247182 33060173 Genome Res. Active retrotransposons help maintain pericentromeric heterochromatin required for faithful cell division. 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).
FBrf0247192 33168136 eLife The Drosophila Individual Activity Monitoring and Detection System (DIAMonDS). 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.
FBrf0247218 33176146 Cell Rep. Intramacrophage ROS Primes the Innate Immune System via JAK/STAT and Toll Activation. 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].
FBrf0247316 33113043 Apoptosis Functional characterization of the Drosophila suzukii pro-apoptotic genes reaper, head involution defective and grim. The binary expression of different pro-apoptotic genes using 2A peptides.
FBrf0247326 33016195 Fly A pipeline for precise and efficient genome editing by sgRNA-Cas9 RNPs in Drosophila. Improved pipeline for CRISPR mediated genome editing in Drosophila species. Generation of new vector to make donor plasmids for homology-directed repair
FBrf0247327 33234068 Open Biol. The application of rapid evaporative ionization mass spectrometry in the analysis of Drosophila species-a potential new tool in entomology. 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
FBrf0247119 32973040 Genome Res. Transposon expression in the Drosophila brain is driven by neighboring genes and diversifies the neural transcriptome. 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.
FBrf0247148 33159074 Nat. Commun. A single-cell atlas and lineage analysis of the adult Drosophila ovary. Single-cell RNA-sequencing dataset of the adult Drosophila ovary containing transcriptome profiles for all major ovarian cell types.
FBrf0247254 33184447 Commun. Biol. A sensitive mNeonGreen reporter system to measure transcriptional dynamics in Drosophila development. 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.
FBrf0247413 33274326 Micropub Biol Evidence of slightly increased Pol II pausing in UPF1-depleted Drosophila melanogaster cells. DRB treatment followed by Pol II ChIP

Nov 2020

FBrf number PubMed ID Journal Title Author description of technical advance
FBrf0246918 32955431 eLife AANAT1 functions in astrocytes to regulate sleep homeostasis. Antibody
FBrf0246897 33036271 Biomedicines Humanization of Drosophila Gαo to Model GNAO1 Paediatric Encephalopathies. Endogenous locus was edited with a two-step CRISPR/Cas9-mediated replacement.
FBrf0246907 32917765 Biol. Open Quantifying Drosophila adults with the use of a smartphone. 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.
FBrf0246919 32783958 J. Insect Physiol. How to use the development of individual Drosophila larvae as a metabolic sensor. We introduce a developmental 96-well plate assay to use individual Drosophila larvae as tool for metabolic studies.
FBrf0247073 33077914 Nat. Genet. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Novel method to compare 3D chromatin conformation data in Drosophila
FBrf0247109 32814018 Neuron Synthesis of Conserved Odor Object Representations in a Random, Divergent-Convergent Network. Comprehensive calcium imaging from all 2,000 Kenyon cells in the mushroom body at single cell resolution.
FBrf0247160 33155978 eLife Modulation of flight and feeding behaviours requires presynaptic IP3Rs in dopaminergic neurons. 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.
FBrf0247169 32916115 Curr. Biol. Collective Cell Sorting Requires Contractile Cortical Waves in Germline Cells. use of Hydrogel for live-imaging of Drosophila ovaries
FBrf0247175 33048531 Anal. Chem. Real-Time Measurement of Stimulated Dopamine Release in Compartments of the Adult Drosophila melanogaster Mushroom Body. 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
FBrf0247184 33163946 iScience Transcription Factor Binding Affinities and DNA Shape Readout. 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.
FBrf0247019 33108408 PLoS ONE Three distinct mechanisms, Notch instructive, permissive, and independent, regulate the expression of two different pericardial genes to specify cardiac cell subtypes. Sequence, features, and schematic of the pWattB-nlacZ reporter construct vector
FBrf0247101 33117817 Front. Cell Dev. Biol. An Immobilization Technique for Long-Term Time-Lapse Imaging of Explanted Drosophila Tissues. A new method for immobilizing explanted Drosophila tissue in agarose for use in long-term live imaging.
FBrf0247149 32955048 Analyst Improving serotonin fast-scan cyclic voltammetry detection: new waveforms to reduce electrode fouling. Using new fast-scan cyclic voltammetry serotonin specific waveforms for in vivo detection of serotonin in Drosophila tissue.
FBrf0247179 33090988 PLoS Biol. Interphase-arrested Drosophila embryos activate zygotic gene expression and initiate mid-blastula transition events at a low nuclear-cytoplasmic ratio. 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.
FBrf0247228 31960114 Cell. Molec. Life Sci. Loss of function in the Drosophila clock gene period results in altered intermediary lipid metabolism and increased susceptibility to starvation. Analysis of the chronometabolome including lipids
FBrf0247230 33177090 Sci. Adv. Persistent epigenetic reprogramming of sweet taste by diet. Transgenic Targeted DamID construct for the gene polycomb-like (Pcl) under the control of a UAS.

Oct 2020

FBrf number PubMed ID Journal Title Author description of technical advance
FBrf0246799 32013401 Biochemistry Subverting Hedgehog Protein Autoprocessing by Chemical Induction of Paracatalysis. 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)
FBrf0246922 32901612 eLife Topology-driven protein-protein interaction network analysis detects genetic sub-networks regulating reproductive capacity. 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.
FBrf0246250 32652492 iScience PhotoGal4: A Versatile Light-Dependent Switch for Spatiotemporal Control of Gene Expression in Drosophila Explants. 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.
FBrf0246808 32973185 Sci. Rep. A novel setup for simultaneous two-photon functional imaging and precise spectral and spatial visual stimulation in Drosophila. 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.
FBrf0246889 32745561 J. Insect Physiol. CRISPR/Cas9 mediated disruption of the white gene leads to pigmentation deficiency and copulation failure in Drosophila suzukii. New white gene mutant strains were generated in Drosophila suzukii and can be used as resources to study the corresponding phenotype.
FBrf0246845 32958931 Nat. Protoc. CRISPR-based engineering of gene knockout cells by homology-directed insertion in polyploid Drosophila S2R+ cells. 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.
FBrf0246864 32759315 J. Virol. Partitiviruses Infecting Drosophila melanogaster and Aedes aegypti Exhibit Efficient Biparental Vertical Transmission. Drosophila melanogaster line infected only with galbut virus (FoCo-17 line 30)
FBrf0246967 33064752 PLoS ONE Comparative proteomics analysis of dietary restriction in Drosophila. The isobaric tags for relative and absolute quantification (iTRAQ) technology was chosen to sequence the proteomes of Drosophila
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