FlyBase:Papers with technical advances
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. | 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 RNAâDNA 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 |