FlyBase:Papers with technical advances

Popular Resource Categories

All Resources

CRISPR

ScRNA-Seq

RNAi

Stocks

Antibodies

Neuroscience

Model Organism Databases

Images

Maps

Protocols

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

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.	[1]	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