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Papers with Technical Advances

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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

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