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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

2024

Oct 2024

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
This protocol involves imaging the same larvae class IV neurons without the use of anesthetics and for a short duration of time using spinning disk confocal microscope.	Protocol for Imaging the Same Class IV Neurons at Different Stages of Development.	Bio Protoc.	39210953	FBrf0260316
LexAop-PiGM-Iq: optogenetic tool to disrupt G protein alpha subunit q signaling through membrane recruitment of a minimal regulator of G protein signaling (RGS) domain.	Selective optogenetic inhibition of Gαq or Gαi signaling by minimal RGS domains disrupts circuit functionality and circuit formation.	Proc. Natl. Acad. Sci. U.S.A.	39190348	FBrf0260277
We present a Hidden Markov Model trained to detect seizure-related behavioral phenotypes in a model for Dup15q syndrome.	Glial expression of Drosophila UBE3A causes spontaneous seizures that can be modulated by 5-HT signaling.	Neurobiol. Disease	39197537	FBrf0260426
Synthetic venerose. 1-O-[4-O-(2-aminoethylphosphate)-Î²-D-galactopyranosyl]-x-glycerol in a R and S isomer mix was custom synthesized by WuXi AppTec Co (China).	A sexually transmitted sugar orchestrates reproductive responses to nutritional stress.	Nat. Commun.	39353950	FBrf0260550
Optimisation of hybridisation-chain reaction (HCR) for imaging single molecules of RNA in drosophila larvae. Includes a free-to-use, customisable probe designer tool and protocol details.	Optimization of hybridization chain reaction for imaging single RNA molecules in Drosophila larvae.	Fly	39351922	FBrf0260562
New platform for generating histone mutant genotypes for use in epigenetic studies.	Redesigning the Drosophila histone gene cluster: an improved genetic platform for spatiotemporal manipulation of histone function.	Genetics	39039029	FBrf0260395
To reach the resolution required to resolve germ granule organization by super resolution microscopy, the distance between the sample and the objective was reduced by slicing the posterior of embryos.	Spatial organization of translation and translational repression in two phases of germ granules.	Nat. Commun.	39271704	FBrf0260451
This paper includes a new type of reagents to study protein complex and protein recruitment in cell culture system.	Dachsous and Fat coordinately repress the Dachs-Dlish-Approximated complex to control growth.	J. Cell Biol.	39373700	FBrf0260621
Isolation of mitotic and meiotic cell populations by FACS based on the restrictive expression pattern and properties of Bam::GFP and Wcd::RFP transgenic proteins. This allowed processing the RNA for high-throughput sequencing.	Transcriptomic analysis of meiotic genes during the mitosis-to-meiosis transition in Drosophila females.	Genetics	39225982	FBrf0260629
This paper shows that BoID technique can be used to identify light-dependent or -induced interaction using Drosophila cell line S2.	Interactions of drosophila cryptochrome.	Photochem. Photobiol.	38314442	FBrf0260474
An interactive online application (Meiotic Navigator) compiling new functional data on male fertility and associated testicular microscopy images of 920 evolutionarily conserved spermatocyte genes is available at https://pages.igc.pt/meionav.	The conserved genetic program of male germ cells uncovers ancient regulators of human spermatogenesis.	eLife	39388236	FBrf0260647

Sep 2024

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
Quantitative analysis of both cuticular and gut microbiotas of D. melanogaster after topical challenge with different strains of the entomopathogenic fungus Metarhizium robertsii.	Engineered fungus containing a caterpillar gene kills insects rapidly by disrupting their ecto- and endo-microbiomes.	Commun. Biol.	39112633	FBrf0260201
We designed TF-High-Evolutionary (TF-HighEvo), a transcription factor (TF) fused with a base editor (activation-induced deaminase), to continuously induce germline mutations at TF-binding sites across regulatory networks in Drosophila.	TF-High-Evolutionary: In Vivo Mutagenesis of Gene Regulatory Networks for the Study of the Genetics and Evolution of the Drosophila Regulatory Genome.	Mol. Biol. Evol.	39117360	FBrf0260285
The method to quantify muscle damage that can be used comparatively across different fly lines and genotypes.	Muscle degeneration in aging Drosophila flies: the role of mechanical stress.	Skelet. Muscle	39164781	FBrf0260281
A panel of 12 transgenic gRNA lines targeting different numbers of non-coding genomic sites (individual gRNAs targeting between two and 53 sites in the diploid genome). gRNAs, expressed ubiquitously under the U6 promoter, were inserted into the attP2 site.	Tolerance thresholds underlie responses to DNA damage during germline development.	Genes Dev.	39054057	FBrf0260254
A CRISPR/Cas9 method for knock-in and knock-out experiments in S2 cells, whereby an antibiotic-resistance gene is inserted in-frame with the coding region of a gene-of interest. We isolate null cells using antibiotics in feeder layers followed by expansion to make clonal lines.	Generating CRISPR-edited clonal lines of cultured Drosophila S2 cells.	Biol Methods Protoc	39206452	FBrf0260333
We have developed a tool (NP-HMMer) to identify neuropeptides based on Hidden Markov Models. Using NP-HMMer we identified phoenixin neuropeptide (CG34242) in Drosophila.	Proteome-wide neuropeptide identification using NeuroPeptide-HMMer (NP-HMMer).	Gen. Comp. Endocrinol.	39084320	FBrf0260384
The Double-Headed EP (DEP) transposon, used for insertional mutagenesis, is a P element derivative. The DEP element has Gal4-activatable, outward-directed UAS-promoters at both ends which can be deleted separately in vivo by the FLP or Cre recombinases, respectively.	Dominant suppressor genes of p53-induced apoptosis in Drosophila melanogaster.	G3 (Bethesda)	38985658	FBrf0260371
We generated a subtype-specific split-Gal4 for pC1a, a subtype of pC1 neurons.	Male cuticular pheromones stimulate removal of the mating plug and promote re-mating through pC1 neurons in Drosophila females.	eLife	39255004	FBrf0260363
Novel concussion model for Drosophila, modified negative geotaxis assay, AI-based tracking of individual flies during negative geotaxis.	Adverse impact of female reproductive signaling on age-dependent neurodegeneration after mild head trauma in Drosophila.	eLife	39213032	FBrf0260349

Aug 2024

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
New protocol for quantifying vacuoles in fly brain.	Protocol to analyze 3D neurodegenerative vacuoles in Drosophila melanogaster.	STAR Protoc	38635393	FBrf0259828
A new PacBio sequencing library construction method named LILAP.	Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes.	Nat. Commun.	38969648	FBrf0259990
Technical guidance on dissection and immunolabeling of 3rd instar larvae.	Dissection and Immunolabeling of the Central and Peripheral Nervous System of Drosophila Larvae.	Cold Spring Harb. Protoc.	37399181	FBrf0259843
Technical description and protocol for proximity ligation assay in 3rd instar larvae.	Proximity Ligation Assay (PLA) for Fillets of Drosophila Larvae.	Cold Spring Harb. Protoc.	37399180	FBrf0259865
Technical description and protocol for cryo-sectioning of Drosophila larvae for greater imaging resolution.	Whole-Larva Cryosectioning and Immunolabeling of Drosophila Larvae.	Cold Spring Harb. Protoc.	37399178	FBrf0259906
Con-DAM integrates the Con-Ex (Consumption-Excretion) assay and the DAM (Drosophila Activity Monitor) into a single unit. We expect Con-DAM to serve as an easy method for various purposes that require quantifying food consumption and sleep/activity in the same individual flies.	Con-DAM: Simultaneous measurement of food intake and sleep in Drosophila at the single fly resolution.	MicroPubl Biol	39005561	FBrf0259963
DNA barcoding is a reliable method for species identification, while traditional morphological identification struggles with cryptic species. DNA barcoding democratizes scientific research by enabling reproducibility and consistency across global studies.	Species identification of livefood flightless fly (Torinido-shoujoubae) through DNA barcoding.	Ecol. Evol.	38979002	FBrf0259947
This protocol provides details on studying plasma membrane stretching in developing Drosophila ovarian cysts using Flipper-TR dye and fluorescence lifetime imaging microscopy.	A protocol for measuring plasma membrane tension in the Drosophila ovary using fluorescence lifetime imaging microscopy.	STAR Protoc	38489272	FBrf0259826
1) Screen for nuclear architecture proteins that are required for peripheral chromatin positioning 2) Interactors of Stwl in cultured cells 3) RNA-seq from female GSC-like cells upon Stwl overexpression 4) CUT&RUN data for genomic targets of Stwl in female GSC-like cells.	A nuclear architecture screen in Drosophila identifies Stonewall as a link between chromatin position at the nuclear periphery and germline stem cell fate.	Genes Dev.	38866555	FBrf0259861
Software for behavioral phenotyping.	LarvaTagger: manual and automatic tagging of Drosophila larval behaviour.	Bioinformatics	38970365	FBrf0260086
Smc1 tag-switch transgene. mCherry tag flanked by FRT sites. Superfolder GFP follows the mCherry cassette. Before FRT expression, Smc1-mCherry is expressed. FRT excision results in expression of Smc1-mCherry. So one can "switch" the tag by inducing FRT expression.	Chromatin-associated cohesin turns over extensively and forms new cohesive linkages in Drosophila oocytes during meiotic prophase.	Curr. Biol.	38870933	FBrf0259933
Smc1 tag-switch transgene. mCherry tag flanked by FRT sites. Superfolder GFP follows the mCherry cassette. Before FRT expression, Smc1-mCherry is expressed. FRT excision results in expression of Smc1-mCherry. So one can "switch" the tag by inducing FRT expression.	Chromatin-associated cohesin turns over extensively and forms new cohesive linkages in Drosophila oocytes during meiotic prophase.	Curr. Biol.	38870933	FBrf0259933
We developed a proteomic method (VESPA, Variant Enabled SILAC Proteomic Analysis) to test the hypothesis that Drosophila male seminal fluid RNA is translated by females.	Females translate male mRNA transferred during mating.	iScience	39108707	FBrf0260210
Transgenic flies with tub-Mer-mNG, tub-MermutCC-mNG, tub-MermutCC-DIX-mNG, tub-MermutCC-FUS-mNG, or tub-GFP-2xOsh2-PH (PI4P reporter).	PI4P-mediated solid-like Merlin condensates orchestrate Hippo pathway regulation.	Science	39116228	FBrf0260187
Characterisation of sperm metabolism during sperm storage application of fluorescence lifetime imaging microscopy.	Drosophila melanogaster sperm turn more oxidative in the female.	J. Exp. Biol.	39023115	FBrf0260184
cMyc-wt and cMyc-5P were generated in this study.	Ribosome stalling during c-myc translation presents actionable cancer cell vulnerability.	PNAS Nexus	39161732	FBrf0260233

Jul 2024

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
Reporter for recruitment of the Male Specific Lethal dosage compensation complex.	Identification of X chromatin is modulated by complementary pathways in Drosophila melanogaster.	G3 (Bethesda)	38491905	FBrf0259697
Gene level promoter evolution rates of genes implicated in transposon silencing, as well as germ cell-specific and somatic cell-specific genes and their relative interspecies expression divergence between D. melanogaster and D. yakuba.	Rapid evolution of promoters from germline-specifically expressed genes including transposon silencing factors.	BMC Genomics	38977960	FBrf0259952
Expansion microscopy (ExM) The following transgenic fly lines: dj-(MTS)tdTomato (red-MD) dj-CPV (sperm plasma membrane) UASp-eGFP-hCD63 rubicon-tdTomato (endogenous tag) UASz-rubicon-eGFP UASz-hCD63-tdTomato	Egg multivesicular bodies elicit an LC3-associated phagocytosis-like pathway to degrade paternal mitochondria after fertilization.	Nat. Commun.	38977659	FBrf0259998
We generated a number of GFP-tagged alleles of the Cheerio gene including point mutations that affect the mechanical signalling of filamin and small deletion that remove one or more protein domains.	Filamin protects myofibrils from contractile damage through changes in its mechanosensory region.	PLoS Genet.	38905299	FBrf0259956
Tripartite FLP recombinase-based conditional transgene expression.	Conditional Inhibition of Eip75B Eliminates the Effects of Mating and Mifepristone on Lifespan in Female Drosophila.	Cells	38994975	FBrf0259922
Strains that express dsRNA to additional 1.688[X] repeats.	siRNA that participates in Drosophila dosage compensation is produced by many 1.688X and 359 bp repeats.	Genetics	38718207	FBrf0259937
Expressing a human KCNJ2 transgene (either classically-used GFP-tagged version or more recently created HA-tagged version; BDSC #6595 or #92026, respectively) inhibits injury-induced calcium influx in neurons and possibly other cell types.	Calcium plays an essential role in early-stage dendrite injury detection and regeneration.	Prog. Neurobiol.	38825174	FBrf0259891
We have designed and manufactured a device to study a highly complex trait such as flight. This device is relatively easy to make and use, as well as inexpensive. We have also developed a suitable software to analyze the traits derived from the videos in a more automated manner.	The relationship between morphology and flight in Drosophila: a study of two pairs of sibling species from a natural population.	Insect Sci.	37689967	FBrf0259792
In this paper, we present Au-doped ZnO nanocrystals (NCs) with enhanced biocompatibility. The study reveals luminescent properties of ZnO:Au NCs, suggesting potential for bioimaging and drug delivery tracking.	Tuning Biocompatibility and Bactericidal Efficacy as a Function of Doping of Gold in ZnO Nanocrystals.	ACS Omega	38799310	FBrf0259601

Jun 2024

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
This atlas of larval VNC cell types describes immature.(future adult VNC) neurons- organized in a trajectory, and mature interneurons, glia and motoneurons. It links individual clusters to known neurons and uncovers new pathways and genes, i.e. ukar - a new glutamate receptor.	scRNA-seq data from the larval Drosophila ventral cord provides a resource for studying motor systems function and development.	Dev. Cell	38569548	FBrf0259499
Novel method for a compound retention in Drosophila, mRNA multiplexing of the Drosophila genes	Sex-specific pharmacokinetic response to phytoestrogens in Drosophila melanogaster.	Biomed. Pharmacotherapy	38663102	FBrf0259642
Protocol for Drosophila nervous system imaging.	Ex Vivo Brain Imaging in Drosophila.	Cold Spring Harb. Protoc.	37197828	FBrf0259614
Protocol for Drosophila nervous system imaging.	Imaging Olfactory Learning-Induced Plasticity in Vivo in the Drosophila Brain.	Cold Spring Harb. Protoc.	37197829	FBrf0259663
Protocol for Drosophila nervous system imaging.	Functional Imaging of Learning-Induced Plasticity in the Central Nervous System with Genetically Encoded Reporters in Drosophila.	Cold Spring Harb. Protoc.	37197830	FBrf0259620
Protocol for Drosophila nervous system imaging.	Modeling neurodegenerative and neurodevelopmental disorders in the Drosophila mushroom body.	Learn. Mem.	38876485	FBrf0259776
Extracellular superoxide dismutase 3 (SOD3) assay with whole ovaries.	Orthologs of NOX5 and EC-SOD/SOD3: dNox and dSod3 Impact Egg Hardening Process and Egg Laying in Reproductive Function of Drosophila melanogaster.	Int. J. Mol. Sci.	38892326	FBrf0259794

May 2024

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
We have used the SBF-SEM to visualize the organelle contacts.	ATF4-dependent increase in mitochondrial-endoplasmic reticulum tethering following OPA1 deletion in skeletal muscle.	J. Cell. Physiol.	38419397	FBrf0259269
A transgenic chromatin interaction peptide-fused Cas9 exhibits higher mutagenesis efficiency. Additionally, a collection of UAS-sgRNAs transgenic flies have been shown to be valuable for chromoconnectome gene manipulation.	Conditional chemoconnectomics (cCCTomics) as a strategy for efficient and conditional targeting of chemical transmission.	eLife	38686992	FBrf0259397
We established improved methods for collecting hemolymph and evaluating its osmolality more accurately and reproducibly.	Refinement of a technique for collecting and evaluating the osmolality of haemolymph from Drosophila larvae.	J. Exp. Biol.	38634259	FBrf0259426
We created a suite of new DSCP-based reporter vectors for diverse insect species, leveraging dual compatibility with piggyBac and PhiC31-integration, the 3xP3 universal eye marker, GATEWAY cloning, different colors of reporters and markers, as well as Gal4-UAS binary expression.	A new suite of reporter vectors and a novel landing site survey system to study cis-regulatory elements in diverse insect species.	Sci. Rep.	38698030	FBrf0259440
Resource: Drosophila adult eye proteome.	Eye proteome of Drosophila melanogaster.	Proteomics	37963819	FBrf0259492
A new drosophila mutant with a loss of function mutation in the gene adipose. The previously used mutant adp[60] line is no longer available and this line adp[1] can replace it in functional studies as it phenocopies the increased fat storage.	A novel adipose loss-of-function mutant in Drosophila.	Fly	38741287	FBrf0259509
This paper references the expression patterns of long non-coding RNAs available on the Fly-FISH database (link to database: https://fly-fish.ccbr.utoronto.ca/).	Spatially revealed roles for lncRNAs in Drosophila spermatogenesis, Y chromosome function and evolution.	Nat. Commun.	38714658	FBrf0259500
It is a new resource.	Embryonic spatiotemporal expression pattern of Folded gastrulation suggests roles in multiple morphogenetic events and regulation by AbdA.	G3 (Bethesda)	38366558	FBrf0259445
A set of IDR alignments across 33 Drosophila genomes where biochemical features of those IDRs have been scored for conservation using models of trait evolution	Evolutionary analyses of intrinsically disordered regions reveal widespread signals of conservation.	PLoS Comput. Biol.	38662765	FBrf0259452

Apr 2024

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
Set of 52 genes were discovered in the paper that interact genetically with rdgB.	A genetic screen to uncover mechanisms underlying lipid transfer protein function at membrane contact sites.	Life Sci Alliance	38499328	FBrf0259024
Method for building a device for administering time- and depth- calibrated closed-head injury to Drosophila.	dTBI2: A Calibrated, Tunable Device for Administering Traumatic Brain Injury in Drosophila.	Curr Protoc	38511393	FBrf0259091
This is a protocol for the mass isolation of staged pupal intestines during Drosophila melanogaster development based on buoyancy in sucrose for biochemical evaluation of protein ubiquitylation. This protocol can be extended to investigate biochemical changes in other tissues.	Mass isolation of staged Drosophila pupal intestines for analysis of protein ubiquitylation.	STAR Protoc	37950865	FBrf0258960
Automatic system for recognizing fly courtship.	An automatic system for recognizing fly courtship patterns via an image processing method.	Behav Brain Funct	38493127	FBrf0259038
Ex-vivo live imaging of Drosophila pupal midgut intestianl stem cell divisions.	A live-imaging protocol for tracking intestinal stem cell divisions in the Drosophila melanogaster pupal midgut.	STAR Protoc	38041821	FBrf0258953
This paper describes an automated robotic microinjection system for Drosophila and zebrafish.	High-throughput genetic manipulation of multicellular organisms using a machine-vision guided embryonic microinjection robot.	Genetics	38373262	FBrf0259210
We have developed a tissue-specific O-GlcNAcylation profiling tool to enrich candidate substrates. Through this tool, we mapped the O-GlcNAc interactome and created an O-GlcNAc atlas for various brain regions of Drosophila (tsOGA, http://www.kyuanlab.com/tsOGA).	Tissue-specific O-GlcNAcylation profiling identifies substrates in translational machinery in Drosophila mushroom body contributing to olfactory learning.	eLife	38619103	FBrf0259241
Split inteins are incorporated into Trojan-exon (Diao F et al, 2015) to make gene specific drivers.	Hox gene-specific cellular targeting using split intein Trojan exons.	Proc. Natl. Acad. Sci. U.S.A.	38602904	FBrf0259289
A method to synchronise female germline stem cell differentiation in vivo, generating sufficient material for 'omics or biochemistry experiments at specified stages of differentiation. The study includes RNA-seq and Ribo-seq from this material, at 6 stages of differentiation.	Two distinct waves of transcriptome and translatome changes drive Drosophila germline stem cell differentiation.	EMBO J.	38480936	FBrf0259258
The use of pseudo-time analysis in single-embryo RNA-sequencing data to determine developmental stage instead of manual embryo staging, thus avoiding human errors. Furthermore, we validated an approach to identify male and female embryos using their transcriptomes.	Single-embryo RNA sequencing for continuous and sex-specific gene expression analysis on Drosophila.	STAR Protoc	37682716	FBrf0258985

Mar 2024

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
Single cell sequencing of pupal to adult midgut development. Provides information about cell types and genes expressed in these as the gut undergoes final adult maturation.	The emergence of circadian timekeeping in the intestine.	Nat. Commun.	38413599	FBrf0258833
A transgene encoding a membrane-tethered form of Noktochor, a protein that is normally secreted from astrocytes and neurons to regulate sleep.	Drosophila noktochor regulates night sleep via a local mushroom body circuit.	iScience	38380256	FBrf0258837
A collection of cell-type-specific stable-split GAL4 reagents for courtship song neurons. https://splitgal4.janelia.org/precomputed/Lillvis%202023.html	Nested neural circuits generate distinct acoustic signals during Drosophila courtship.	Curr. Biol.	38295797	FBrf0258823
A new drug stabilizable GAL80ds variant was created by fusing it to a low-background DHFR-22-DD.	A drug stabilizable GAL80[ds] for conditional control of gene expression via GAL4-UAS and CRISPR-Cas9 systems in Drosophila.	Sci. Rep.	38467687	FBrf0259011
Transformer female-specific introns from three speices (D. melanogaster, D. suzukii, and C. capitata) were tested to show female-specificity at different developmental stages in D. melanogaster. This can be used for female-specific expression study.	A Fluorescent Sex-Sorting Technique for Insects with the Demonstration in Drosophila melanogaster.	GEN Biotechnol	38415050	FBrf0258926
We generated a tool kit to express each Zika virus protein in Drosophila.	A Zika virus protein expression screen in Drosophila to investigate targeted host pathways during development.	Dis. Model Mech.	38214058	FBrf0258902
A protocol for studying the neural circuit of female receptivity in Drosophila.	A protocol for measuring the sexual receptivity of female Drosophila.	STAR Protoc	37703181	FBrf0259009
We have developed a glyoxal-based fast fixation method for IF, FISH and FISH-IF in Drosophila embryos. We also show that some antibodies like Bic-D, Dynein Heavy Chain and a-Actinin that failed to stain in formaldehyde fixed embryos, were stained beautifully with glyoxal fixation	Glyoxal-based fixation of Drosophila embryos for immunofluorescence staining and RNA in situ hybridization.	STAR Protoc	37405926	FBrf0258995
New Ca2+ imaging probes targets to subcellular compartments.	Ca[2+] imaging of synaptic compartments using subcellularly targeted GCaMP8f in Drosophila.	STAR Protoc	38198278	FBrf0259069

Feb 2024

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
Laser capture microdissection of Drosophila Lymph gland.	A conserved nutrient responsive axis mediates autophagic degradation of miRNA-mRNA hybrids in blood cell progenitors.	Nucleic Acids Res.	37994707	FBrf0258524
Single-cell transcriptome.	Ribogenesis boosts controlled by HEATR1-MYC interplay promote transition into brain tumour growth.	EMBO Rep.	38225354	FBrf0258545
dsRNA complexation with diblock copolymers is a promising strategy for RNAi-based species-specific knock down of gene expression.	Effective delivery and selective insecticidal activity of double-stranded RNA via complexation with diblock copolymer varies with polymer block composition.	Pest Manag. Sci.	37759365	FBrf0258536
We present a combined light microscopy, micro-computed tomography (micro-CT), and Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) approach for high-resolution correlative three-dimensional (3D; volume imaging) to characterize internal soft, delicate tissues.	Three-dimensional correlative microscopy of the Drosophila female reproductive tract reveals modes of communication in seminal receptacle sperm storage.	Commun. Biol.	38321098	FBrf0258684
We have generated new UAS-APEX2-GBP strains to facilitate high resolution analysis of any GFP-tagged protein that is expressed in somatic D. melanogaster tissues by electron microscopy.	Basal spot junctions of Drosophila epithelial tissues respond to morphogenetic forces and regulate Hippo signaling.	Dev. Cell	38134928	FBrf0258581
mRNA pellet/EDTA-pellet ratio calculation. Pellet: mRNA-trapping ribosomes; EDTA-pellet: assemblysomes from RNCs. Shift, e.g., elevated DmBLM pellet/EDTA-pellet post-X-ray, indicates assemblysome to ribosome shift, ensuring swift BLM protein access during DNA damage.	1,6-Hexanediol Is Inducing Homologous Recombination by Releasing BLM from Assemblysomes in Drosophila melanogaster.	Int. J. Mol. Sci.	38338890	FBrf0258769
Protocol describes how to perform live imaging of male meiotic cytokinesis in individual spermatocyte cysts and in intact adult testes.	Live Imaging and Analysis of Meiotic Cytokinesis in Drosophila Testes.	Bio Protoc.	38268980	FBrf0258608
Comprehensive resource of stocks for genetic analysis of all protein coding genes on the 4th chromosome.	Fourth Chromosome Resource Project: a comprehensive resource for genetic analysis in Drosophila that includes humanized stocks.	Genetics	37981656	FBrf0258725
Advanced light sheet microscopy technique based on convolutional neural networks to augment live-imaging data with deep-tissue images taken on fixed samples.	Image restoration of degraded time-lapse microscopy data mediated by near-infrared imaging.	Nat. Methods	38177507	FBrf0258736
A method called DISSECT offers the opportunity to extract automatically, in strongly deformed epithelia, a precise characterization of the spatial organization of a given cytoskeletal network combined with morphological quantifications in highly remodeled three-dimensional (3D) epithelial tissues.	DISSECT is a tool to segment and explore cell and tissue mechanics in highly deformed 3D epithelia.	Dev. Cell	37586367	FBrf0257870

Jan 2024

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
Visual Conditional Learning.	A New Behavioral Paradigm for Visual Classical Conditioning in Drosophila.	Bio Protoc.	37969763	FBrf0258115
The paper presents an algorithm to quantify image resolution (quality) as a function of depth. The method is demonstrated on microscopy stacks of Drosophila brains using various imaging parameters. An open source ImageJ plugin implementation is made available.	mtFRC: depth-dependent resolution quantification of image features in 3D fluorescence microscopy.	Bioinform Adv	38146539	FBrf0258342
This paper describes the methods to express and purify catalytically active Drosophila insulin receptor kinase domain and its mutants from insect cells. Enzyme characterization was done using biochemical techniques including in-vitro kinase and thermal shift assays.	Biochemical characterization of the Drosophila insulin receptor kinase and longevity-associated mutants.	FASEB J.	38071609	FBrf0258264
A novel analysis framework for genetic signatures of neuronal phenotypes.	Factorized discriminant analysis for genetic signatures of neuronal phenotypes.	Front. Neuroinform.	38156117	FBrf0258365
Expansion microscopy of epithelial tissues (airways) in embryos.	A surfactant lipid layer of endosomal membranes facilitates airway gas filling in Drosophila.	Curr. Biol.	37992718	FBrf0258245
TubULAR is a tissue cartography tool that maps whole-organ tissue deformations on dynamic surfaces and decomposes them into interpretable components.	TubULAR: tracking in toto deformations of dynamic tissues via constrained maps.	Nat. Methods	38057529	FBrf0258287
This paper develops a graph neural network model for inferring Drosophila gene regulatory networks. Some interactions recorded in flybase are used as evidence to support our computational inferring results. Our model assigns a high prediction score to these gene interactions.	MIGGRI: A multi-instance graph neural network model for inferring gene regulatory networks for Drosophila from spatial expression images.	PLoS Comput. Biol.	37939200	FBrf0258170
We generated 3XHA labeled EcI genomic knock-in stock to indicate the expression pattern of EcI. We made UAS-E22O and UAS-E22O-NRT transgenic flies to degenerate the ecdysteroids. We generated phm-T2A-Gal4, spok-Gal80 to specifically manipulate the gene expression in DIOMs.	Eclosion muscles secrete ecdysteroids to initiate asymmetric intestinal stem cell division in Drosophila.	Dev. Cell	38096823	FBrf0258487
We construct Pros::GFP KI flies to show the endogenous Pros distribution in pupal intestinal stem cells.	Apical-basal polarity precisely determines intestinal stem cell number by regulating Prospero threshold.	Cell Rep.	36773292	FBrf0257653
Generated transgenic UAS-human PPFIA3 reference and variant fly alleles.	A syndromic neurodevelopmental disorder caused by rare variants in PPFIA3.	Am. J. Hum. Genet.	38181735	FBrf0258489
We have reported for the first time, the enhancer activity pattern of olf413 in late pupal brain and have demonstrated that olf413 function is essential for motor activity, gravity sensing and spatial balancing of the body against gravity during climbing.	olf413, a putative octopamine biosynthesis pathway gene is required for negative geotactic motor function in Drosophila melanogaster.	J. Genet.	38073169	FBrf0258269
We designed a conduction-dominated cryomesh to cryopreserve Drosophila embryos for long-term storage. It increased the hatch rate after rewarming at least 3 times higher than the previous Nylon mesh-based cryopreservation.	Conduction-Dominated Cryomesh for Organism Vitrification.	Adv Sci (Weinh)	38018294	FBrf0258552

2023

Dec 2023

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
GeneSwitch.	An Adapted GeneSwitch Toolkit for Comparable Cellular and Animal Models: A Proof of Concept in Modeling Charcot-Marie-Tooth Neuropathy.	Int. J. Mol. Sci.	38003325	FBrf0258128
New single cell genomics atlas of the Drosophila larval eye disc.	A single cell genomics atlas of the Drosophila larval eye reveals distinct photoreceptor developmental timelines.	Nat. Commun.	37938573	FBrf0258045
Miniaturized ultrasound device For Drosophila brain stimulation.	A Miniature Ultrasound Source for Neural Modulation.	IEEE Trans Ultrason Ferroelectr Freq Control	37812556	FBrf0257932
New technique: Use of split-GFP to indicate when a transmembrane protein is inserted into the cell membrane. GFP(11) is added to the extracellular domain of the protein of interest; secreted-GFP(1-10) is expressed outside the cell of interest (for example, by fat bodies).	Coordination of Pickpocket ion channel delivery and dendrite growth in Drosophila sensory neurons.	PLoS Genet.	37943859	FBrf0258102
Introduced a Yolked Control Paradigm for Drosophila Sleep Deprivation Experiments to Account for the Sleep-Independent Effects of Mechanical Deprivation.	Homeostatic control of deep sleep and molecular correlates of sleep pressure in Drosophila.	eLife	37906092	FBrf0258058
CUT&Tag profiling of RNA polymerase II and active and repressive histone modifications in the male germline detailing the timing of gene activation.	Chromosome-specific maturation of the epigenome in the Drosophila male germline.	eLife	38032818	FBrf0258215
Materials used in biosensors.	Nanoporous MoS2 Field-Effect Transistor Based Artificial Olfaction: Achieving Enhanced Volatile Organic Compound Detection Inspired by the Drosophila Olfactory System.	ACS Nano	37902651	FBrf0258166

Nov 2023

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
An alternative method for isolating hemolymph and hemocytes from single Drosophila melanogaster adult flies.	A Simple Protocol for Isolating Hemolymph from Single Drosophila melanogaster Adult Flies.	Methods Protoc	37888032	FBrf0257920
Real-time imaging of exosome and dense-core granule biogenesis using Drosophila secondary cells.	A Rab6 to Rab11 transition is required for dense-core granule and exosome biogenesis in Drosophila secondary cells.	PLoS Genet.	37844085	FBrf0257910
It describes an open source hardware solution to record and manipulate the behaviour of Drosophila larvae and adults. It describes an open source software to track both on-line and off-line the behaviour of Drosophila larvae and adults.	OptoPi: An open source flexible platform for the analysis of small animal behaviour.	HardwareX	37795340	FBrf0257761
A bicistronic transgene in multiple binary expression systems for labeling active zones and cell membranes with only one construct.	SynLight: a bicistronic strategy for simultaneous active zone and cell labeling in the Drosophila nervous system.	G3 (Bethesda)	37757863	FBrf0258005
Single-cell RNA sequencing datasets of embryos at gastrulation.	Single-cell transcriptomics illuminates regulatory steps driving anterior-posterior patterning of Drosophila embryonic mesoderm.	Cell Rep.	37858470	FBrf0257948
We created an easy to use executable file to analyze data from the DAM system.	HoTDAM! An easy-to-use automated assay expands the inducible thermotolerance phenotype in Drosophila melanogaster: Heat hardening reduces motility.	Comp. Biochem. Physiol. A, Mol. Integr. Physiol.	37742820	FBrf0257831

Oct 2023

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
A tool called PL-Seq to investigate genes of interest for coordinated 3' alternative polyadenylation and alternative splicing.	Coordination of alternative splicing and alternative polyadenylation revealed by targeted long read sequencing.	Nat. Commun.	37679364	FBrf0257510
We describe a protocol to perform RNA FISH on polytene chromosomes, in combination with immunofluorescence, to detect protein-locus colocalization.	A hybrid RNA FISH immunofluorescence protocol on Drosophila polytene chromosomes.	BMC Res. Notes	37679799	FBrf0257523
Drosophila as a model organism to determine DNA damage response pathways induced by environmental contaminants.	ATM/Chk2 and ATR/Chk1 Pathways Respond to DNA Damage Induced by Movento[®] 240SC and Envidor[®] 240SC Keto-Enol Insecticides in the Germarium of Drosophila melanogaster.	Toxics	37755764	FBrf0257673
C. elegans expressing Drosophila SVIP.	Tubular lysosome induction couples animal starvation to healthy aging.	Nat Aging	37580394	FBrf0257584
Panel of Drosophila TAFAZZIN mutants in 10 genetically distinct backgrounds as a new resource for testing emerging therapeutics for the treatment of Barth Syndrome while accounting for the influence of genetic diversity on efficacy.	A novel panel of Drosophila TAFAZZIN mutants in distinct genetic backgrounds as a resource for therapeutic testing.	PLoS ONE	37756350	FBrf0257669
Identification of protein interactions	Conformational changes in the negative arm of the circadian clock correlate with dynamic interactomes involved in post-transcriptional regulation.	Cell Rep.	37043358	FBrf0257722
Single cell RNA-sequencing dataset of pupal Drosophila hemocytes.	Single-cell transcriptomics identifies new blood cell populations in Drosophila released at the onset of metamorphosis.	Development	37681301	FBrf0257675
Behavior tracking protocol.	Methods for Exploring the Circuit Basis of Ethanol-Induced Changes in Drosophila Group Locomotor Activity.	Cold Spring Harb. Protoc.	37019608	FBrf0257704
Behavior tracking protocol.	Ethanol Behavioral Responses in Drosophila.	Cold Spring Harb. Protoc.	37019606	FBrf0257681
ChIP-nexus, ChIP-seq, ATAC-seq, and MNase-seq data were generated. Mutant ATAC-seq data were generated. Deep learning models trained on ChIP-nexus and ATAC-seq datasets were generated (https://zenodo.org/record/8075860). Binding motifs for transcription factors were mapped.	Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation.	Dev. Cell	37557175	FBrf0257743
Live imaging with FUCCI cell cycle phase reporters for limited periods in many cells was used to measure the average duration of each phase and hence, division rate for a given cell population. Also, H2B-RFP pulse-chase.	Spatial regulation of Drosophila ovarian Follicle Stem Cell division rates and cell cycle transitions.	PLoS Genet.	37747936	FBrf0257769
Microfluidic technology to automate and standardize the dissociation of CNS tissue into viable neurons for primary culture	Drosophila CASK regulates brain size and neuronal morphogenesis, providing a genetic model of postnatal microcephaly suitable for drug discovery.	Neural Dev.	37805506	FBrf0257764
Transcriptional profile of larval and adult astrocytes	Actin-dependent astrocytic infiltration is a key step for axon defasciculation during remodeling.	Cell Rep.	36790930	FBrf0257708
Method for making tandem duplications of an existing gene.	Demonstration of in vivo engineered tandem duplications of varying sizes using CRISPR and recombinases in Drosophila melanogaster.	G3 (Bethesda)	37462278	FBrf0257718
Detailed instructions on how to work with FRET sensors in intact fly organs.	Metabolic FRET sensors in intact organs: Applying spectral unmixing to acquire reliable signals.	Biol. Open	37671927	FBrf0257767
Four supervised machine-learning models were used to analyze the trajectories of three mutants and Canton-S during exploratory activity.	Drosophila genotypes can be predicted from their exploration locomotive trajectories using supervised machine learning.	Behav. Processes	37717930	FBrf0257793

Sep 2023

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
Endogenously tagged Fs(1)h.	Stepwise modifications of transcriptional hubs link pioneer factor activity to a burst of transcription.	Nat. Commun.	37563108	FBrf0257271
We describe a novel method for conditional protein aggregation that results in nearly instantaneous protein inactivation. This technique is immediately applicable to any GFP-tagged protein.	Evidence that tissue recoil in the early Drosophila embryo is a passive not active process.	Mol. Biol. Cell	37405768	FBrf0257294
Recombination mediated cassette exchange (RMCE) of MiMIC cassette insertion within the Sex Peptide Receptor (SPR) allele for a LexA::QFAD expressing cassette.	Heterogeneous receptor expression underlies non-uniform peptidergic modulation of olfaction in Drosophila.	Nat. Commun.	37644052	FBrf0257390
Toxicology Screening approach Applications of metabolomics Applications of genomics.	Perspectives on the Drosophila melanogaster Model for Advances in Toxicological Science.	Curr Protoc	37639638	FBrf0257380
Optogenetic control over terminal patterning combined with live imaging of target gene transcription and protein accumulation.	Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the early Drosophila embryo.	Development	37602510	FBrf0257429
The snRNA-seq dataset has been made publicly available at DRSC/TRiP Functional Genomics Resources data portal (link) to allow users to query the expression of any gene of interest in thoraces.	REPTOR and CREBRF encode key regulators of muscle energy metabolism.	Nat. Commun.	37582831	FBrf0257286
We have developed a better system for measurement of thermal preference in Drosophila flies. In our paper we describe the potential pitfalls of a measuring device and demonstrate how to perform thermal preference assay in a careful way.	Wolbachia has subtle effects on thermal preference in highly inbred Drosophila melanogaster which vary with life stage and environmental conditions.	Sci. Rep.	37612420	FBrf0257370
Several UAS-driven transgenes, including: - Zdk1 domain targeted to the outer mitochondrial membrane (via dMiro TM domain) for association to LOV2-tagged proteins - mCherry-tagged dMiro (RE isoform) - mCherry/LOV2-tagged dMiro (RE isoform) aa 1-642.	Optogenetic cleavage of the Miro GTPase reveals the direct consequences of real-time loss of function in Drosophila.	PLoS Biol.	37590319	FBrf0257379
Python program for designing triplex-forming oligonucleotides for RNA targets.	TFOFinder: Python program for identifying purine-only double-stranded stretches in the predicted secondary structure(s) of RNA targets.	PLoS Comput. Biol.	37624852	FBrf0257547
In this study, we developed a system to isolate large amounts of tissues from staged Drosophila melanogaster during development based on buoyancy in sucrose for biochemical evaluation of protein ubiquitination.	PINK1, Keap1, and Rtnl1 regulate selective clearance of endoplasmic reticulum during development.	Cell	37633267	FBrf0257587
splitgal4.org (link): This is a centralized database for the gene-specific split-GAL4 lines generated by this study (~100 split-GAL4 lines!) and others in the fly community.	Using single-cell RNA sequencing to generate predictive cell-type-specific split-GAL4 reagents throughout development.	Proc. Natl. Acad. Sci. U.S.A.	37523539	FBrf0257150

Aug 2023

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
Software/code.	Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome.	Science	37384691	FBrf0256956
We build a substrate-laden wheel upon which Drosophila can walk and lay eggs, while we record neural activity. The wheel may be useful to study other behaviors involving substrate interactions. We also build several chamber setups to study aspects of egg-laying behavior in flies.	A rise-to-threshold process for a relative-value decision.	Nature	37407812	FBrf0257087
Gene manipulation in both the Drosophila cardiac model and human induced pluripotent stem cell cardiomyocytes identified interactions between phospholamban/sarcolamban and NCX in the control of cardiac rhythm.	Multiplatform modeling of atrial fibrillation identifies phospholamban as a central regulator of cardiac rhythm.	Dis. Model Mech.	37293707	FBrf0257020
Generation of transgenic fly lines that can express human DHX9.	Heterozygous loss-of-function DHX9 variants are associated with neurodevelopmental disorders: Human genetic and experimental evidences.	Eur J Med Genet	37369308	FBrf0257121
An automated transport robot that can move crawling larvae around an arena for long-term controlled experiments.	Continuous, long-term crawling behavior characterized by a robotic transport system.	eLife	37535068	FBrf0257220
As new resource, in this paper, we report a single-cell transcriptome atlas of Drosophila gastrulae, divided into 77 transcriptomically distinct clusters. With this scRNA-seq data, the genome-wide and accurate spatial patterns of gene expression were also reconstructed.	Single-cell transcriptome atlas of Drosophila gastrula 2.0.	Cell Rep.	37433294	FBrf0257125
New approach based on CRIPSPR-Cas9 technique to generate partial or complete deletions of the Y chromosome.	Y chromosome toxicity does not contribute to sex-specific differences in longevity.	Nat. Ecol. Evol.	37308701	FBrf0257212
The paper reports stripe as an immediate early gene. It includes data showing that endogenous stripe mRNA or protein expression, or stripe-GAL4 (sr[md710])-driven reporter expression can be used as a neural activity marker.	Cell assembly analysis of neural circuits for innate behavior in Drosophila melanogaster using an immediate early gene stripe/egr-1.	Proc. Natl. Acad. Sci. U.S.A.	37549285	FBrf0257229

Jul 2023

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
Botulinum neurotoxin engineered for Gal4-mediated expression. When expressed in neurons, silences both evoked and spontaneous release.	Physiologic and Nanoscale Distinctions Define Glutamatergic Synapses in Tonic vs Phasic Neurons.	J. Neurosci.	37221096	FBrf0256863
We are providing a fully automated computational tool that performs a molecular evolution analysis (detection of positive selection) of any Drosophila melanogaster gene using mostly long-read assemblies of publicly available Drosophila clade genomes.	FREEDA: An automated computational pipeline guides experimental testing of protein innovation.	J. Cell Biol.	37358475	FBrf0256908
Software to analyze rhythmic feeding.	CRUMB: a shiny-based app to analyze rhythmic feeding in Drosophila using the FLIC system.	F1000Res.	37396048	FBrf0256911
A healthy and stable increased fat storage phenotype in Drosophila melanogaster induced by a protein restricted diet.	A protein restricted diet induces a stable increased fat storage phenotype in flies.	Toxicol Rep	37396850	FBrf0256923
Imaging larval tissue differentiation.	Differentiation and function of cardiac valves in the adult Drosophila heart.	J. Exp. Biol.	37306013	FBrf0256950
Advanced MARZ algorithm for analysis of DNA sequences.	Investigating the sequence landscape in the Drosophila initiator core promoter element using an enhanced MARZ algorithm.	PeerJ	37366427	FBrf0256894
A single-cell atlas of the male first tarsal segment during pupal development.	A single-cell atlas of the sexually dimorphic Drosophila foreleg and its sensory organs during development.	PLoS Biol.	37379332	FBrf0256994
Rbp4-Gal4 germline driver that activates in meiotic cells.	Rbp4-Gal4, a germline driver that activates in meiosis, reveals functions for VCP in spermatid development.	Fly	37436409	FBrf0257022
FruC fine-tunes gene transcription by promoting low-levels of H3K27me accumulation.	Low-level repressive histone marks fine-tune gene transcription in neural stem cells.	eLife	37314324	FBrf0257033
Describes an in vitro morphogen gradient reconstitution system.	Reconstitution of morphogen shuttling circuits.	Sci. Adv.	37436981	FBrf0257046
Machine learning-based automatic fly-behavioral detection and annotation (MAFDA) system; anti-FruALL antibody.	Integrating lipid metabolism, pheromone production and perception by Fruitless and Hepatocyte Nuclear Factor 4.	Sci. Adv.	37390217	FBrf0256900
Optimization of the Gal80DD tool for maximal repression of Gal4 expression of RNAi during developmental stages.	An optimized temporally controlled Gal4 system in Drosophila reveals degeneration caused by adult-onset neuronal Vps13D knockdown.	Front. Neurosci.	37457002	FBrf0257041

Jun 2023

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
A novel AstA33-Gal4 line that predominantly targets all AstA enteroendocrine cells in the gut but very limited AstA neurons in the brain.	Gut AstA mediates sleep deprivation-induced energy wasting in Drosophila.	Cell Discov.	37221172	FBrf0256538
High speed voltage imaging with VsLFM.	Virtual-scanning light-field microscopy for robust snapshot high-resolution volumetric imaging.	Nat. Methods	37024654	FBrf0256521
The technique involved forming a whole-cell recording on an MB neuron and applying an electrical stimulus to AL neurons to induce evoked EPSPs from AL to MB.	Efficient strategies based on behavioral and electrophysiological methods for epilepsy-related gene screening in the Drosophila model.	Front. Mol. Neurosci.	37152436	FBrf0256425
Proteomic approach to identify changes in cysteine availability using Drosophila cells or tissue samples based on iodo-TMT probes. This technique can be used to identify potential redox changes at specific cysteine residues proteome-wide under different experimental conditions.	Proteome-wide quantitative analysis of redox cysteine availability in the Drosophila melanogaster eye reveals oxidation of phototransduction machinery during blue light exposure and age.	Redox Biol.	37146512	FBrf0256685
We developed a machine learning (SVR) model for the Drosophila DPR (downstream promoter region, which spans from +17 to +35 nt relative to the +1 transcription start site). The SVR model can be used to predict the transcriptional activity of any test sequence.	Analysis of the Drosophila and human DPR elements reveals a distinct human variant whose specificity can be enhanced by machine learning.	Genes Dev.	37163335	FBrf0256650
Full-length mRNA sequencing in Drosophila tissues (heads, ovaries, embryos at14-16h and 18-22 AEL) and new annotation of transcript isoforms in the indicated tissues.	Sites of transcription initiation drive mRNA isoform selection.	Cell	37178687	FBrf0256598
Refined method for charactering the small RNA pools expressed in different cell niche in Drosophila ovaries. The method was originally described in Malone, et al., Cell, 2009 (PMID: 19395010).	The absence of core piRNA biogenesis factors does not impact efficient transposon silencing in Drosophila.	PLoS Biol.	37279192	FBrf0256641
Single cell RNAseq resource of adult elav>tauR406W brain tissue.	Tau polarizes an aging transcriptional signature to excitatory neurons and glia.	eLife	37219079	FBrf0256723
Live imaging of ex vivo larval NMJ.	Drosophila motor neuron boutons remodel through membrane blebbing coupled with muscle contraction.	Nat. Commun.	37291089	FBrf0256774
Genetic tools that allow visualization and genetic manipulations of cells in the lineage of the adult-type fat body (AFB) from early in metamorphosis.	Dynamic de novo adipose tissue development during metamorphosis in Drosophila melanogaster.	Development	37092314	FBrf0256560
Resource: Single cell transcriptomic analysis of neuroblast lineages at 105h after larval hatching.	Asynchronous transcription and translation of neurotransmitter-related genes characterize the initial stages of neuronal maturation in Drosophila.	PLoS Biol.	37205703	FBrf0256708
A cell-type specific conditionally tagged DLG1 fly that allows for labeling of excitatory postsynapses in identified cells.	A conditional strategy for cell-type-specific labeling of endogenous excitatory synapses in Drosophila.	Cell Rep Methods	37323572	FBrf0256821
NOX::GFP reporter line: The Nox::GFP reporter is generated by replacing NoxCRIMIC.TG4.0 allele with the Double Header GFP/T2A-Gal4-coding cassette following the exact cross scheme of Li-Kroeger et al. (2018).	The bHLH-PAS transcriptional complex Sim:Tgo plays active roles in late oogenesis to promote follicle maturation and ovulation.	Development	37218521	FBrf0256841

May 2023

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
We have developed a new software, which is called LabGym, for automated quantification of animal behaviors across species including Drosophila.	LabGym: Quantification of user-defined animal behaviors using learning-based holistic assessment.	Cell Rep Methods	37056376	FBrf0256265
Chemical probes for SRS imaging of lacZ and Ggt-1 enzyme activity.	Activatable Raman Probes Utilizing Enzyme-Induced Aggregate Formation for Selective Ex Vivo Imaging.	J. Am. Chem. Soc.	37057960	FBrf0256364
A FIJI/ImageJ-based tool to automatically segment and analyze images of active zones and periactive zones of Drosophila neuromuscular junctions. This tool could likely be used for segmentation and analysis of other mesh-like protein distributions within cells.	An approach for quantitative mapping of synaptic periactive zone architecture and organization.	Mol. Biol. Cell	36542486	FBrf0256457
scRNA-seq for mitochondrial derivative in Drosophila testis.	Single-cell RNA-sequencing reveals the transcriptional landscape of ND-42 mediated spermatid elongation via mitochondrial derivative maintenance in Drosophila testes.	Redox Biol.	36933391	FBrf0256499
TaDa-seq for identification of loci where DAxud1 locates using Dam-DAxud1 fusion protein with Illumina NGS.	Drosophila DAxud1 Has a Repressive Transcription Activity on Hsp70 and Other Heat Shock Genes.	Int. J. Mol. Sci.	37108646	FBrf0256390
High resolution chromatin contact Micro-C map on wing imaginal disc.	GAGA-associated factor fosters loop formation in the Drosophila genome.	Mol. Cell	37003261	FBrf0256430
A novel optogenetic Gal4-UAS system (ltLightOn) based on a single light-switchable transactivator, termed GAVPOLT, which dimerizes and binds to gene promoters to activate transgene expression upon blue light illumination.	A Single-Component Optogenetic Gal4-UAS System Allows Stringent Control of Gene Expression in Zebrafish and Drosophila.	ACS Synth. Biol.	36891673	FBrf0256042

Apr 2023

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
Histopathological examination of axonal morphology and Nissl substance using Klüver Luxol Fast Blue-stained tissues.	Attenuation of Seizures, Cognitive Deficits, and Brain Histopathology by Phytochemicals of Imperata cylindrica (L.) P. Beauv (Poaceae) in Acute and Chronic Mutant Drosophila melanogaster Epilepsy Models.	J Evid Based Integr Med	36866635	FBrf0255908
This publication describes an operationally simple single-embryo RNA-sequencing methodology, analysis pipeline and the resulting data from the DGRP-737 fly strain. The method lets users assess transcriptional events during fly embryogenesis in a continuous manner.	Continuous transcriptome analysis reveals novel patterns of early gene expression in Drosophila embryos.	Cell Genom	36950383	FBrf0256068
New Gal4-driver, active in cardiac valve cells.	Tailup expression in Drosophila larval and adult cardiac valve cells.	genesis	36546531	FBrf0256076
(1) large-scale FlyBi ORF clone resource in Gateway format, (2) FlyBi yeast two hybrid data resource, (3) Drosophila Reference Interactome (DroRI), a protein-protein interaction data from multiple datasets at comparable quality accessible at the DRSC MIST online resource.	Next-generation large-scale binary protein interaction network for Drosophila melanogaster.	Nat. Commun.	37061542	FBrf0256286
A modified method for time-lapse imaging of ovarian egg chamber explants, adapted to visualize centripetal migration during oogenesis stages 10A-11	Two phases for centripetal migration of Drosophila melanogaster follicle cells: initial ingression followed by epithelial migration.	Development	36807509	FBrf0256237
We prepared a bacteria-conditioned diet in which bacterial products are enriched in a standard yeast-based fly diet.	Recognition of commensal bacterial peptidoglycans defines Drosophila gut homeostasis and lifespan.	PLoS Genet.	37023169	FBrf0256280
The article introduces the IMBA (Individual Maggot Behaviour Analyser), a new, free software to track and analyse the behaviour of individual Drosophila larvae tested in groups. This can be used for quick phenotypic analyses of mutations and other genetic manipulations.	High-resolution analysis of individual Drosophila melanogaster larvae uncovers individual variability in locomotion and its neurogenetic modulation.	Open Biol.	37072034	FBrf0256288
Cell ablation via laser microsurgery; volume electron microscopy; electrophysiology.	Co-option of epidermal cells enables touch sensing.	Nat. Cell Biol.	36959505	FBrf0256245
Streptavidin-based reversible protein retention system, RUSH ("retention using selective hooks").	Acute manipulation and real-time visualization of membrane trafficking and exocytosis in Drosophila.	Dev. Cell	37023749	FBrf0256302
Population recordings of descending neurons during behavior.	Ascending neurons convey behavioral state to integrative sensory and action selection brain regions.	Nat. Neurosci.	36959417	FBrf0256179
Generation of an automatically quantified axonal degeneration program based on Python that combines a pre-trained deep-learning masking tool with an axon terminal counting tool.	Direct evaluation of neuroaxonal degeneration with the causative genes of neurodegenerative diseases in Drosophila using the automated axon quantification system, MeDUsA.	Hum. Mol. Genet.	36611008	FBrf0256313
Computational approach for transposable element detection in long-reads.	TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.	Genome Biol.	37013657	FBrf0256182
PGA-dependent OPP incorporation (POPPi) for rapid visualization and identification of nascent protein synthesis.	Rapid cell type-specific nascent proteome labeling in Drosophila.	eLife	37092974	FBrf0256333
We present a method and Python module for automatically counting and measuring optical parameters of compound eyes in 2D microscope images and 3D datasets such as those generated by microCT.	Measuring compound eye optics with microscope and microCT images.	Commun. Biol.	36882636	FBrf0255994

Mar 2023

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
A computational resource for the Drosophila community to consult prior to experimental studies investigating the epigenetic regulatory networks of miRNA-PcG/trxG mediated gene expression.	A genome-wide computational approach to define microRNA-Polycomb/trithorax gene regulatory circuits in Drosophila.	Dev. Biol.	36596335	FBrf0255654
Newly developed transgenic lines used in this study help in Live imaging of Muscle stem cells in Drosophila together with neighbouring tissues.	Dual-Color Live Imaging of Adult Muscle Stem Cells in the Embryonic Tissues of Drosophila melanogaster.	Bio Protoc.	36816994	FBrf0255866
We have generated novel deletions, duplications, and inversions of the cis-regulatory domains of the bithorax complex using genome editing and frt technology.	CRISPR/Cas9 and FLP-FRT mediated regulatory dissection of the BX-C of Drosophila melanogaster.	Chromosome Res.	36719476	FBrf0255637
It showed how apoptosis was affected when the expression level of heme oxygenase was changed. It includes the analyses (assays/experiments) that were exploited to show this particular effect in the fruit fly model organism.	The dual role of heme oxygenase in regulating apoptosis in the nervous system of Drosophila melanogaster.	Front. Physiol.	36860519	FBrf0255944
New polyclonal antibody for BRAHMA protein.	CLOCK and TIMELESS regulate rhythmic occupancy of the BRAHMA chromatin-remodeling protein at clock gene promoters.	PLoS Genet.	36809369	FBrf0255960
We established a method for accurate and high throughput measurement and sorting of viable Drosophila egg size using large particle flow cytometry.	A high throughput method for egg size measurement in Drosophila.	Sci. Rep.	36882448	FBrf0255918
This genetic toolkit can be used to convert Gal4 strains into LexA and Flippase transgenes through simple genetic crosses and fluorescence screening.	A toolkit for converting Gal4 into LexA and Flippase transgenes in Drosophila.	G3 (Bethesda)	36617215	FBrf0255992
We generated and described the first protocol to measure the ALR, autophagic lysosomal reformation, in vivo in Drosophila larval tissues. SMER28 has been identified as a positive modulator of ALR in Drosophila and rescues the Drosophila spg15 model.	Rescue of lysosomal function as therapeutic strategy for SPG15 hereditary spastic paraplegia.	Brain	36029068	FBrf0255931
Two new techniques to study glycogen granules: 1) staining in fixed tissues to reveal their subcellular organization 2) a glycogenin-YFP to follow their dynamics live.	Drosophila embryos spatially sort their nutrient stores to facilitate their utilization.	Development	36805634	FBrf0256031
74,000 CNS images with stochastic single neuron (MultiColor FlpOut; MCFO) labeling within GAL4 patterns, searchable by shape at https://neuronbridge.janelia.org and suitable for predicting likely split-GAL4 combinations.	A searchable image resource of Drosophila GAL4 driver expression patterns with single neuron resolution.	eLife	36820523	FBrf0256048
Bioinformatic method for identifying functionally active cis-regulatory modules using Cut&Run datasets together with other publicly available chromatin profiling data.	Distinct roles for canonical and variant histone H3 lysine-36 in Polycomb silencing.	Sci. Adv.	36857457	FBrf0255964

Feb 2023

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
We have generated fly lines that express a luciferase reporter construct for clock gene transcriptional activity. The luciferase reporters are FLP-inducible, which enables cell specificity, and luciferase expression is dictated by a minimal E-box sequence from the period gene.	Inducible Reporter Lines for Tissue-specific Monitoring of Drosophila Circadian Clock Transcriptional Activity.	J. Biol. Rhythms	36495136	FBrf0255523
New way to immobilize and image the larva.	Bending Drosophila larva using a microfluidic device enables imaging of its brain and nervous system at single neuronal resolution.	Lab Chip	36537269	FBrf0255467
We tagged endogenous Runt locus with LlamaTag (Bothma et al., Cell, 2019), which binds to eGFP, to quantify the nuclear concentration of Runt protein in vivo. We reported the concentration dynamics of Runt protein in nuclear cycles of 13 and 14, in males and females.	Predictive modeling reveals that higher-order cooperativity drives transcriptional repression in a synthetic developmental enhancer.	eLife	36503705	FBrf0255484
Generation of nanobodies against sarcomeric proteins.	A nanobody toolbox to investigate localisation and dynamics of Drosophila titins and other key sarcomeric proteins.	eLife	36645120	FBrf0255573
RNA-seq analysis identified DGC-dependent genes as well as genes whose differential expression patterns under stress are perturbed in DGC mutants. This work is a valuable resource for research into the etiology of muscular dystrophy symptoms.	Signaling through the dystrophin glycoprotein complex affects the stress-dependent transcriptome in Drosophila.	Dis. Model Mech.	36594281	FBrf0255683
This paper uses a previously described chemical compound to inhibit the RNA methylase function of the human protein FTSJ1. Here we show that the same compound, called DAP, acts on the orthologous Drosophila proteins Trm7_32 and Trm7_34 (here through larval feeding).	The ribose methylation enzyme FTSJ1 has a conserved role in neuron morphology and learning performance.	Life Sci Alliance	36720500	FBrf0255635
Single molecule RNA FISH in third instar Drosophila eye discs.	Buffered EGFR signaling regulated by spitz-to-argos expression ratio is a critical factor for patterning the Drosophila eye.	PLoS Genet.	36730442	FBrf0255752
GST-IVTT (PMID: 36102272).	Plk4 Is a Novel Substrate of Protein Phosphatase 5.	Int. J. Mol. Sci.	36768356	FBrf0255743
Application of DNA-PAINT super resolution microscopy to study sarcomere morphology. Use of Nanobodies for DNA-PAINT	Nanobodies combined with DNA-PAINT super-resolution reveal a staggered titin nanoarchitecture in flight muscles.	eLife	36645127	FBrf0255622
We present a protocol combining the advantages of high-pressure freezing and freeze substitution and direct stochastic optical reconstruction microscopy to quantify nanotopology of the AZ scaffold protein Bruchpilot at neuromuscular junctions of Drosophila melanogaster.	Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila melanogaster after Rapid Cryofixation.	Int. J. Mol. Sci.	36768451	FBrf0255755
Novel method to carry out dye-exclusion assay in adult Drosophila to test for BBB integrity.	Optimization and Technical Considerations for the Dye-Exclusion Protocol Used to Assess Blood-Brain Barrier Integrity in Adult Drosophila melanogaster.	Int. J. Mol. Sci.	36768206	FBrf0255731
Single fly quantification of tissue-specific insulin signaling by measuring epitope-tagged phospho-Akt in an ELISA method.	A genetic strategy to measure insulin signaling regulation and physiology in Drosophila.	PLoS Genet.	36730473	FBrf0255740
This paper provides a resource of transcriptionally repressive protein domains in Drosophila melanogaster transcription factors.	Systematic identification and characterization of repressive domains in Drosophila transcription factors.	EMBO J.	36545802	FBrf0255657
https://bis.zju.edu.cn/DCL/, single-cell RNA landscape of Drosophila.	Construction of a cross-species cell landscape at single-cell level.	Nucleic Acids Res.	35929025	FBrf0255582
The catalogue of putative Cp190- and/or CTCF-dependent chromatin insulator elements.	Topological screen identifies hundreds of Cp190- and CTCF-dependent Drosophila chromatin insulator elements.	Sci. Adv.	36735780	FBrf0255702
Usage of a single experimental setup that is unique, distinctive and cost-effective using minimal laboratory equipment and resources in order to quantify percent lethality, lifespan and the crawling and climbing behaviour of genetically perturbed or toxicant-exposed Drosophila.	A Reliable and Consistent Method to Quantify Percent Lethality and Life Span in Drosophila melanogaster.	Bio Protoc.	36789168	FBrf0255786

Jan 2023

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
Botulinum neurotoxin engineered for Gal4-mediated expression. When expressed in neurons, silences both evoked and spontaneous release.	A glutamate receptor C-tail recruits CaMKII to suppress retrograde homeostatic signaling.	Nat. Commun.	36496500	FBrf0255253
Mass spectrometry analysis of ubiquitination status and chain-type from isolated mitochondria immunofluorescence staining for Serine65 phosphorylated ubiquitin (pS65-Ub) on muscle tissue	Parkin drives pS65-Ub turnover independently of canonical autophagy in Drosophila.	EMBO Rep.	36250243	FBrf0255201
Mathematical modelling.	Coupling cell proliferation rates to the duration of recruitment controls final size of the Drosophila wing.	Proc. Biol. Sci.	36476003	FBrf0255229
Actin was chased using a new dye.	Synthesis of First Coumarin Fluorescent Dye for Actin Visualization.	Bioconjug. Chem.	36264777	FBrf0255043
Removal of single cells from living tissues followed by transcriptome analysis.	Direct isolation of single cells from living brains of Drosophila melanogaster without dissociation for transcriptome analysis.	STAR Protoc	36181682	FBrf0255279
Expression of dDAT cDNA in HEK293 suspension cultures using baculovirus for transduction. Measuring substrate and inhibitor affinities on purified protein by Scintillation Proximity Assay (SPA).	Pharmacological Characterization of Purified Full-Length Dopamine Transporter from Drosophila melanogaster.	Cells	36497070	FBrf0255233
Protocol for purifications of exosomal proteins using size exclusion chromatography.	Purification of exosome-enriched proteins produced in a Drosophila cell line by size exclusion chromatography.	STAR Protoc	36386877	FBrf0255029
The expression of prokaryotic NMN-Deamindase (NMN-D) alters the nicotinamide adenine dinucleotide (NAD+) metabolic flux in vivo, by lowering the precursor nicotinamide mononucleotide (NMN).	The NAD+ precursor NMN activates dSarm to trigger axon degeneration in Drosophila.	eLife	36476387	FBrf0255352
ubi-RNase H1::GFP transgenic fly line - C-terminally GFP-tagged coding sequence of RNase H1 (rnh1) expressed from the poly-ubiquitin promoter based pUWG vector.	Drosophila pVALIUM10 TRiP RNAi lines cause undesired silencing of Gateway-based transgenes.	Life Sci Alliance	36446522	FBrf0255152
High resolution single cell RNA sequencing resource data from 1-day, 3-day and 7-day old adult eyes from Canton S. Novel cell type specific marker genes were identified for each major eye cell types and some marker genes were validated in vivo.	Single cell RNA sequencing of the adult Drosophila eye reveals distinct clusters and novel marker genes for all major cell types.	Commun. Biol.	36517671	FBrf0255275
A new method of recording calcium influx response of tmc-Gal4 labeled md-L neuron in drosophila labellum in vivo, imaging the cell soma in real time and defecting the taste hair to apply mechanical stimuli.	Drosophila proboscis extension response and GCaMP imaging for assaying food appeal based on grittiness.	STAR Protoc	36386873	FBrf0255042
A developmental time course of synapse addition in multiple classes of ORNs, PNs, and LNs in the Drosophila antennal lobe represents a new resource for the field.	Synaptic Development in Diverse Olfactory Neuron Classes Uses Distinct Temporal and Activity-Related Programs.	J. Neurosci.	36446587	FBrf0255430
Generated transgenic UAS-human EIF4A2 reference and variant fly alleles.	Rare EIF4A2 variants are associated with a neurodevelopmental disorder characterized by intellectual disability, hypotonia, and epilepsy.	Am. J. Hum. Genet.	36528028	FBrf0255452
Gene expression evolution tool that is easy to run and should become popular.	Stochastic Modeling of Gene Expression Evolution Uncovers Tissue- and Sex-Specific Properties of Expression Evolution in the Drosophila Genus.	J. Comput. Biol.	36037023	FBrf0255437
Hi speed planar illumination microscopy.	Polyphasic circadian neural circuits drive differential activities in multiple downstream rhythmic centers.	Curr. Biol.	36610393	FBrf0255503
Ablation of individual cells within a tissue by two-photon microscopy and live imaging of tissue responses with confocal microscopy.	Photoablation at single cell resolution and its application in the Drosophila epidermis and peripheral nervous system.	Front. Physiol.	36685184	FBrf0255529
RT&Tag uses antibodies to tether tagmentation reagents in situ in the nucleus for profiling of localized RNAs. The method has been used for profiling RNAs associated with silenced or active chromatin, or with RNA modifications.	The Drosophila embryo as a tabula rasa for the epigenome.	Fac Rev	36644296	FBrf0255473

2022

Dec 2022

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
A procedure for single molecule RNA fluorescent in situ hybridization for imaging of Clk transcript localization in whole-mount brains (e.g., lLNv, DN), with experiment protocols and an automated Snakemake analysis workflow. Presumed to be adaptable to other transcripts.	Streamlined single-molecule RNA-FISH of core clock mRNAs in clock neurons in whole mount Drosophila brains.	Front. Physiol.	36439243	FBrf0255126
Genetically encoded luminescence reporter of distinct circadian clock oscillations in target neurons and tissues, in vivo, in real time.	Real time, in vivo measurement of neuronal and peripheral clocks in Drosophila melanogaster.	eLife	36190119	FBrf0254983
'Expansion Microscopy' is used to improve the resolution of images of cells, and in this study, we developed a technique to determine the mitochondrial morphology within germline stem cells.	Expansion Microscopy-based imaging for visualization of mitochondria in Drosophila ovarian germline stem cells.	FEBS Open Bio	36331359	FBrf0255206
The new algorithm Transposable Element Finder (TEF) enables the detection of TE transpositions, even for TEs with an unknown sequence.	Transposable element finder (TEF): finding active transposable elements from next generation sequencing data.	BMC Bioinformatics	36418944	FBrf0255150
Auxin inducible-degradation GFP-tagged allele of Med19.	Inducible degradation of the Drosophila Mediator subunit Med19 reveals its role in regulating developmental but not constitutively-expressed genes.	PLoS ONE	36445897	FBrf0255104

Nov 2022

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

Oct 2022

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

Sep 2022

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

Aug 2022

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

Jul 2022

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

Jun 2022

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

May 2022

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

Apr 2022

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

Mar 2022

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

Feb 2022

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

Jan 2022

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

2021

Dec 2021

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

Nov 2021

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

Oct 2021

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

Sep 2021

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

Aug 2021

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

Jul 2021

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

Jun 2021

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

May 2021

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

Apr 2021

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

Mar 2021

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

Feb 2021

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

Jan 2021

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

2020

Dec 2020

Author description of technical advance	Title	Journal	PubMed ID	FBrf number
Analysis of Gal4 expression patterns of commonly used Gal4 drivers in adult females.	Analysis of Gal4 Expression Patterns in Adult Drosophila Females.	G3 (Bethesda)	32917721	FBrf0247159
We defined the origins of repeat-derived RNAs and their specific chromatin locations in Drosophila S2 cells using the global 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

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+{| class="wikitable"
+|-
+! ''Author description of technical advance''!!''Title''!!''Journal''!!''PubMed ID''!! ''FBrf number''
+|-
+| This protocol involves imaging the same larvae class IV neurons without the use of anesthetics and for a short duration of time using spinning disk confocal microscope.||Protocol for Imaging the Same Class IV Neurons at Different Stages of Development.||Bio Protoc.||[https://pubmed.ncbi.nlm.nih.gov/39210953  39210953 ]||[https://flybase.org/reports/FBrf0260316 FBrf0260316]
+|- bgcolor="lightgrey"
+| LexAop-PiGM-Iq: optogenetic tool to disrupt G protein alpha subunit q signaling through membrane recruitment of a minimal regulator of G protein signaling (RGS) domain.||Selective optogenetic inhibition of Gαq or Gαi signaling by minimal RGS domains disrupts circuit functionality and circuit formation.||Proc. Natl. Acad. Sci. U.S.A.||[https://pubmed.ncbi.nlm.nih.gov/39190348  39190348 ]||[https://flybase.org/reports/FBrf0260277 FBrf0260277]
+|-
+| We present a Hidden Markov Model trained to detect seizure-related behavioral phenotypes in a model for Dup15q syndrome. ||Glial expression of Drosophila UBE3A causes spontaneous seizures that can be modulated by 5-HT signaling.||Neurobiol. Disease||[https://pubmed.ncbi.nlm.nih.gov/39197537  39197537 ]||[https://flybase.org/reports/FBrf0260426 FBrf0260426]
+|- bgcolor="lightgrey"
+| Synthetic venerose. 1-O-[4-O-(2-aminoethylphosphate)-Î²-D-galactopyranosyl]-x-glycerol in a R and S isomer mix was custom synthesized by WuXi AppTec Co (China). ||A sexually transmitted sugar orchestrates reproductive responses to nutritional stress.||Nat. Commun.||[https://pubmed.ncbi.nlm.nih.gov/39353950  39353950 ]||[https://flybase.org/reports/FBrf0260550 FBrf0260550]
+|-
+| Optimisation of hybridisation-chain reaction (HCR) for imaging single molecules of RNA in drosophila larvae. Includes a free-to-use, customisable probe designer tool and protocol details.||Optimization of hybridization chain reaction for imaging single RNA molecules in Drosophila larvae.||Fly||[https://pubmed.ncbi.nlm.nih.gov/39351922  39351922 ]||[https://flybase.org/reports/FBrf0260562 FBrf0260562]
+|- bgcolor="lightgrey"
+| New platform for generating histone mutant genotypes for use in epigenetic studies.||Redesigning the Drosophila histone gene cluster: an improved genetic platform for spatiotemporal manipulation of histone function.||Genetics||[https://pubmed.ncbi.nlm.nih.gov/39039029  39039029 ]||[https://flybase.org/reports/FBrf0260395 FBrf0260395]
+|-
+| To reach the resolution required to resolve germ granule organization by super resolution microscopy, the distance between the sample and the objective was reduced by slicing the posterior of embryos.||Spatial organization of translation and translational repression in two phases of germ granules.||Nat. Commun.||[https://pubmed.ncbi.nlm.nih.gov/39271704  39271704 ]||[https://flybase.org/reports/FBrf0260451 FBrf0260451]
+|- bgcolor="lightgrey"
+| This paper includes a new type of reagents to study protein complex and protein recruitment in cell culture system.||Dachsous and Fat coordinately repress the Dachs-Dlish-Approximated complex to control growth.||J. Cell Biol.||[https://pubmed.ncbi.nlm.nih.gov/39373700  39373700 ]||[https://flybase.org/reports/FBrf0260621 FBrf0260621]
+|-
+| Isolation of mitotic and meiotic cell populations by FACS based on the restrictive expression pattern and properties of Bam::GFP and Wcd::RFP transgenic proteins. This allowed processing the RNA for high-throughput sequencing.||Transcriptomic analysis of meiotic genes during the mitosis-to-meiosis transition in Drosophila females.||Genetics||[https://pubmed.ncbi.nlm.nih.gov/39225982  39225982 ]||[https://flybase.org/reports/FBrf0260629 FBrf0260629]
+|- bgcolor="lightgrey"
+| This paper shows that BoID technique can be used to identify light-dependent or -induced interaction using Drosophila cell line S2.||Interactions of drosophila cryptochrome.||Photochem. Photobiol.||[https://pubmed.ncbi.nlm.nih.gov/38314442  38314442 ]||[https://flybase.org/reports/FBrf0260474 FBrf0260474]
+|-
+| An interactive online application (Meiotic Navigator) compiling new functional data on male fertility and associated testicular microscopy images of 920 evolutionarily conserved spermatocyte genes is available at https://pages.igc.pt/meionav. ||The conserved genetic program of male germ cells uncovers ancient regulators of human spermatogenesis.||eLife||[https://pubmed.ncbi.nlm.nih.gov/39388236  39388236 ]||[https://flybase.org/reports/FBrf0260647 FBrf0260647]
+|- bgcolor="lightgrey"
+|}
+==== Sep 2024====
+{| class="wikitable"
+|-
+! ''Author description of technical advance''!!''Title''!!''Journal''!!''PubMed ID''!! ''FBrf number''
+|-
+| Quantitative analysis of both cuticular and gut microbiotas of D. melanogaster after topical challenge with different strains of the entomopathogenic fungus Metarhizium robertsii.||Engineered fungus containing a caterpillar gene kills insects rapidly by disrupting their ecto- and endo-microbiomes.||Commun. Biol.||[https://pubmed.ncbi.nlm.nih.gov/39112633  39112633 ]||[https://flybase.org/reports/FBrf0260201 FBrf0260201]
+|- bgcolor="lightgrey"
+| We designed TF-High-Evolutionary (TF-HighEvo), a transcription factor (TF) fused with a base editor (activation-induced deaminase), to continuously induce germline mutations at TF-binding sites across regulatory networks in Drosophila.||TF-High-Evolutionary: In Vivo Mutagenesis of Gene Regulatory Networks for the Study of the Genetics and Evolution of the Drosophila Regulatory Genome.||Mol. Biol. Evol.||[https://pubmed.ncbi.nlm.nih.gov/39117360  39117360 ]||[https://flybase.org/reports/FBrf0260285 FBrf0260285]
+|-
+| The method to quantify muscle damage that can be used comparatively across different fly lines and genotypes.||Muscle degeneration in aging Drosophila flies: the role of mechanical stress.||Skelet. Muscle||[https://pubmed.ncbi.nlm.nih.gov/39164781  39164781 ]||[https://flybase.org/reports/FBrf0260281 FBrf0260281]
+|- bgcolor="lightgrey"
+| A panel of 12 transgenic gRNA lines targeting different numbers of non-coding genomic sites (individual gRNAs targeting between two and 53 sites in the diploid genome). gRNAs, expressed ubiquitously under the U6 promoter, were inserted into the attP2 site.||Tolerance thresholds underlie responses to DNA damage during germline development.||Genes Dev.||[https://pubmed.ncbi.nlm.nih.gov/39054057  39054057 ]||[https://flybase.org/reports/FBrf0260254 FBrf0260254]
+|-
+| A CRISPR/Cas9 method for knock-in and knock-out experiments in S2 cells, whereby an antibiotic-resistance gene is inserted in-frame with the coding region of a gene-of interest. We isolate null cells using antibiotics in feeder layers followed by expansion to make clonal lines.||Generating CRISPR-edited clonal lines of cultured Drosophila S2 cells.||Biol Methods Protoc||[https://pubmed.ncbi.nlm.nih.gov/39206452  39206452 ]||[https://flybase.org/reports/FBrf0260333 FBrf0260333]
+|- bgcolor="lightgrey"
+| We have developed a tool (NP-HMMer) to identify neuropeptides based on Hidden Markov Models. Using NP-HMMer we identified phoenixin neuropeptide (CG34242) in Drosophila. ||Proteome-wide neuropeptide identification using NeuroPeptide-HMMer (NP-HMMer).||Gen. Comp. Endocrinol.||[https://pubmed.ncbi.nlm.nih.gov/39084320  39084320 ]||[https://flybase.org/reports/FBrf0260384 FBrf0260384]
+|-
+| The Double-Headed EP (DEP) transposon, used for insertional mutagenesis, is a P element derivative. The DEP element has Gal4-activatable, outward-directed UAS-promoters at both ends which can be deleted separately in vivo by the FLP or Cre recombinases, respectively. ||Dominant suppressor genes of p53-induced apoptosis in Drosophila melanogaster.||G3 (Bethesda)||[https://pubmed.ncbi.nlm.nih.gov/38985658  38985658 ]||[https://flybase.org/reports/FBrf0260371 FBrf0260371]
+|- bgcolor="lightgrey"
+| We generated a subtype-specific split-Gal4 for pC1a, a subtype of pC1 neurons.||Male cuticular pheromones stimulate removal of the mating plug and promote re-mating through pC1 neurons in Drosophila females.||eLife||[https://pubmed.ncbi.nlm.nih.gov/39255004  39255004 ]||[https://flybase.org/reports/FBrf0260363 FBrf0260363]
+|-
+| Novel concussion model for Drosophila, modified negative geotaxis assay, AI-based tracking of individual flies during negative geotaxis. ||Adverse impact of female reproductive signaling on age-dependent neurodegeneration after mild head trauma in Drosophila.||eLife||[https://pubmed.ncbi.nlm.nih.gov/39213032  39213032 ]||[https://flybase.org/reports/FBrf0260349 FBrf0260349]
+|- bgcolor="lightgrey"
+|}
+==== Aug 2024====
+{| class="wikitable"
+|-
+! ''Author description of technical advance''!!''Title''!!''Journal''!!''PubMed ID''!! ''FBrf number''
+|-
+| New protocol for quantifying vacuoles in fly brain.||Protocol to analyze 3D neurodegenerative vacuoles in Drosophila melanogaster.||STAR Protoc||[https://pubmed.ncbi.nlm.nih.gov/38635393  38635393 ]||[https://flybase.org/reports/FBrf0259828 FBrf0259828]
+|- bgcolor="lightgrey"
+| A new PacBio sequencing library construction method named LILAP.||Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes.||Nat. Commun.||[https://pubmed.ncbi.nlm.nih.gov/38969648  38969648 ]||[https://flybase.org/reports/FBrf0259990 FBrf0259990]
+|-
+| Technical guidance on dissection and immunolabeling of 3rd instar larvae.||Dissection and Immunolabeling of the Central and Peripheral Nervous System of Drosophila Larvae.||Cold Spring Harb. Protoc.||[https://pubmed.ncbi.nlm.nih.gov/37399181  37399181 ]||[https://flybase.org/reports/FBrf0259843 FBrf0259843]
+|- bgcolor="lightgrey"
+| Technical description and protocol for proximity ligation assay in 3rd instar larvae.||Proximity Ligation Assay (PLA) for Fillets of Drosophila Larvae.||Cold Spring Harb. Protoc.||[https://pubmed.ncbi.nlm.nih.gov/37399180  37399180 ]||[https://flybase.org/reports/FBrf0259865 FBrf0259865]
+|-
+| Technical description and protocol for cryo-sectioning of Drosophila larvae for greater imaging resolution. ||Whole-Larva Cryosectioning and Immunolabeling of Drosophila Larvae.||Cold Spring Harb. Protoc.||[https://pubmed.ncbi.nlm.nih.gov/37399178  37399178 ]||[https://flybase.org/reports/FBrf0259906 FBrf0259906]
+|- bgcolor="lightgrey"
+| Con-DAM integrates the Con-Ex (Consumption-Excretion) assay and the DAM (Drosophila Activity Monitor) into a single unit. We expect Con-DAM to serve as an easy method for various purposes that require quantifying food consumption and sleep/activity in the same individual flies.||Con-DAM: Simultaneous measurement of food intake and sleep in Drosophila at the single fly resolution.||MicroPubl Biol||[https://pubmed.ncbi.nlm.nih.gov/39005561  39005561 ]||[https://flybase.org/reports/FBrf0259963 FBrf0259963]
+|-
+| DNA barcoding is a reliable method for species identification, while traditional morphological identification struggles with cryptic species. DNA barcoding democratizes scientific research by enabling reproducibility and consistency across global studies.||Species identification of livefood flightless fly (Torinido-shoujoubae) through DNA barcoding.||Ecol. Evol.||[https://pubmed.ncbi.nlm.nih.gov/38979002  38979002 ]||[https://flybase.org/reports/FBrf0259947 FBrf0259947]
+|- bgcolor="lightgrey"
+| This protocol provides details on studying plasma membrane stretching in developing Drosophila ovarian cysts using Flipper-TR dye and fluorescence lifetime imaging microscopy.||A protocol for measuring plasma membrane tension in the Drosophila ovary using fluorescence lifetime imaging microscopy.||STAR Protoc||[https://pubmed.ncbi.nlm.nih.gov/38489272  38489272 ]||[https://flybase.org/reports/FBrf0259826 FBrf0259826]
+|-
+| 1) Screen for nuclear architecture proteins that are required for peripheral chromatin positioning 2) Interactors of Stwl in cultured cells 3) RNA-seq from female GSC-like cells upon Stwl overexpression 4) CUT&RUN data for genomic targets of Stwl in female GSC-like cells.||A nuclear architecture screen in Drosophila identifies Stonewall as a link between chromatin position at the nuclear periphery and germline stem cell fate.||Genes Dev.||[https://pubmed.ncbi.nlm.nih.gov/38866555  38866555 ]||[https://flybase.org/reports/FBrf0259861 FBrf0259861]
+|- bgcolor="lightgrey"
+| Software for behavioral phenotyping.||LarvaTagger: manual and automatic tagging of Drosophila larval behaviour.||Bioinformatics||[https://pubmed.ncbi.nlm.nih.gov/38970365  38970365 ]||[https://flybase.org/reports/FBrf0260086 FBrf0260086]
+|-
+| Smc1 tag-switch transgene.  mCherry tag flanked by FRT sites.  Superfolder GFP follows the mCherry cassette.  Before FRT expression, Smc1-mCherry is expressed.  FRT excision results in expression of Smc1-mCherry.  So one can "switch" the tag by inducing FRT expression. ||Chromatin-associated cohesin turns over extensively and forms new cohesive linkages in Drosophila oocytes during meiotic prophase.||Curr. Biol.||[https://pubmed.ncbi.nlm.nih.gov/38870933  38870933 ]||[https://flybase.org/reports/FBrf0259933 FBrf0259933]
+|- bgcolor="lightgrey"
+| Smc1 tag-switch transgene.  mCherry tag flanked by FRT sites.  Superfolder GFP follows the mCherry cassette.  Before FRT expression, Smc1-mCherry is expressed.  FRT excision results in expression of Smc1-mCherry.  So one can "switch" the tag by inducing FRT expression. ||Chromatin-associated cohesin turns over extensively and forms new cohesive linkages in Drosophila oocytes during meiotic prophase.||Curr. Biol.||[https://pubmed.ncbi.nlm.nih.gov/38870933  38870933 ]||[https://flybase.org/reports/FBrf0259933 FBrf0259933]
+|-
+| We developed a proteomic method (VESPA, Variant Enabled SILAC Proteomic Analysis) to test the hypothesis that Drosophila male seminal fluid RNA is translated by females. ||Females translate male mRNA transferred during mating.||iScience||[https://pubmed.ncbi.nlm.nih.gov/39108707  39108707 ]||[https://flybase.org/reports/FBrf0260210 FBrf0260210]
+|- bgcolor="lightgrey"
+| Transgenic flies with tub-Mer-mNG, tub-MermutCC-mNG, tub-MermutCC-DIX-mNG, tub-MermutCC-FUS-mNG, or tub-GFP-2xOsh2-PH (PI4P reporter).||PI4P-mediated solid-like Merlin condensates orchestrate Hippo pathway regulation.||Science||[https://pubmed.ncbi.nlm.nih.gov/39116228  39116228 ]||[https://flybase.org/reports/FBrf0260187 FBrf0260187]
+|-
+| Characterisation of sperm metabolism during sperm storage application of fluorescence lifetime imaging microscopy.||Drosophila melanogaster sperm turn more oxidative in the female.||J. Exp. Biol.||[https://pubmed.ncbi.nlm.nih.gov/39023115  39023115 ]||[https://flybase.org/reports/FBrf0260184 FBrf0260184]
+|- bgcolor="lightgrey"
+| cMyc-wt and cMyc-5P were generated in this study.||Ribosome stalling during c-myc translation presents actionable cancer cell vulnerability.||PNAS Nexus||[https://pubmed.ncbi.nlm.nih.gov/39161732  39161732 ]||[https://flybase.org/reports/FBrf0260233 FBrf0260233]
+|-
+|}
+==== Jul 2024====
+{| class="wikitable"
+|-
+! ''Author description of technical advance''!!''Title''!!''Journal''!!''PubMed ID''!! ''FBrf number''
+|-
+| Reporter for recruitment of the Male Specific Lethal dosage compensation complex.||Identification of X chromatin is modulated by complementary pathways in Drosophila melanogaster.||G3 (Bethesda)||[https://pubmed.ncbi.nlm.nih.gov/38491905  38491905 ]||[https://flybase.org/reports/FBrf0259697 FBrf0259697]
+|- bgcolor="lightgrey"
+| Gene level promoter evolution rates of genes implicated in transposon silencing, as well as germ cell-specific and somatic cell-specific genes and their relative interspecies expression divergence between D. melanogaster and D. yakuba.||Rapid evolution of promoters from germline-specifically expressed genes including transposon silencing factors.||BMC Genomics||[https://pubmed.ncbi.nlm.nih.gov/38977960  38977960 ]||[https://flybase.org/reports/FBrf0259952 FBrf0259952]
+|-
+| Expansion microscopy (ExM) The following transgenic fly lines: dj-(MTS)tdTomato (red-MD) dj-CPV (sperm plasma membrane) UASp-eGFP-hCD63 rubicon-tdTomato (endogenous tag) UASz-rubicon-eGFP UASz-hCD63-tdTomato||Egg multivesicular bodies elicit an LC3-associated phagocytosis-like pathway to degrade paternal mitochondria after fertilization.||Nat. Commun.||[https://pubmed.ncbi.nlm.nih.gov/38977659  38977659 ]||[https://flybase.org/reports/FBrf0259998 FBrf0259998]
+|- bgcolor="lightgrey"
+| We generated a number of GFP-tagged alleles of the Cheerio gene including point mutations that affect the mechanical signalling of filamin and small deletion that remove one or more protein domains.||Filamin protects myofibrils from contractile damage through changes in its mechanosensory region.||PLoS Genet.||[https://pubmed.ncbi.nlm.nih.gov/38905299  38905299 ]||[https://flybase.org/reports/FBrf0259956 FBrf0259956]
+|-
+| Tripartite FLP recombinase-based conditional transgene expression.||Conditional Inhibition of Eip75B Eliminates the Effects of Mating and Mifepristone on Lifespan in Female Drosophila.||Cells||[https://pubmed.ncbi.nlm.nih.gov/38994975  38994975 ]||[https://flybase.org/reports/FBrf0259922 FBrf0259922]
+|- bgcolor="lightgrey"
+| Strains that express dsRNA to additional 1.688[X] repeats.||siRNA that participates in Drosophila dosage compensation is produced by many 1.688X and 359 bp repeats.||Genetics||[https://pubmed.ncbi.nlm.nih.gov/38718207  38718207 ]||[https://flybase.org/reports/FBrf0259937 FBrf0259937]
+|-
+| Expressing a human KCNJ2 transgene (either classically-used GFP-tagged version or more recently created HA-tagged version; BDSC #6595 or #92026, respectively) inhibits injury-induced calcium influx in neurons and possibly other cell types.||Calcium plays an essential role in early-stage dendrite injury detection and regeneration.||Prog. Neurobiol.||[https://pubmed.ncbi.nlm.nih.gov/38825174  38825174 ]||[https://flybase.org/reports/FBrf0259891 FBrf0259891]
+|- bgcolor="lightgrey"
+|  We have designed and manufactured a device to study a highly complex trait such as flight. This device is relatively easy to make and use, as well as inexpensive. We have also developed a suitable software to analyze the traits derived from the videos in a more automated manner.||The relationship between morphology and flight in Drosophila: a study of two pairs of sibling species from a natural population.||Insect Sci.||[https://pubmed.ncbi.nlm.nih.gov/37689967  37689967 ]||[https://flybase.org/reports/FBrf0259792 FBrf0259792]
+|-
+| In this paper, we present Au-doped ZnO nanocrystals (NCs) with enhanced biocompatibility. The study reveals luminescent properties of ZnO:Au NCs, suggesting potential for bioimaging and drug delivery tracking.||Tuning Biocompatibility and Bactericidal Efficacy as a Function of Doping of Gold in ZnO Nanocrystals.||ACS Omega||[https://pubmed.ncbi.nlm.nih.gov/38799310  38799310 ]||[https://flybase.org/reports/FBrf0259601 FBrf0259601]
+|- bgcolor="lightgrey"
+|}
+==== Jun 2024====
+{| class="wikitable"
+|-
+! ''Author description of technical advance''!!''Title''!!''Journal''!!''PubMed ID''!! ''FBrf number''
+|-
+| This atlas of larval VNC cell types describes immature.(future adult VNC) neurons- organized in a trajectory, and mature interneurons, glia and motoneurons. It links individual clusters to known neurons and uncovers new pathways and genes, i.e. ukar - a new glutamate receptor. ||scRNA-seq data from the larval Drosophila ventral cord provides a resource for studying motor systems function and development.||Dev. Cell||[https://pubmed.ncbi.nlm.nih.gov/38569548  38569548 ]||[https://flybase.org/reports/FBrf0259499 FBrf0259499]
+|- bgcolor="lightgrey"
+| Novel method for a compound retention in Drosophila, mRNA multiplexing of the Drosophila genes||Sex-specific pharmacokinetic response to phytoestrogens in Drosophila melanogaster.||Biomed. Pharmacotherapy||[https://pubmed.ncbi.nlm.nih.gov/38663102  38663102 ]||[https://flybase.org/reports/FBrf0259642 FBrf0259642]
+|-
+| Protocol for Drosophila nervous system imaging.||Ex Vivo Brain Imaging in Drosophila.||Cold Spring Harb. Protoc.||[https://pubmed.ncbi.nlm.nih.gov/37197828  37197828 ]||[https://flybase.org/reports/FBrf0259614 FBrf0259614]
+|- bgcolor="lightgrey"
+| Protocol for Drosophila nervous system imaging.||Imaging Olfactory Learning-Induced Plasticity in Vivo in the Drosophila Brain.||Cold Spring Harb. Protoc.||[https://pubmed.ncbi.nlm.nih.gov/37197829  37197829 ]||[https://flybase.org/reports/FBrf0259663 FBrf0259663]
+|-
+| Protocol for Drosophila nervous system imaging.||Functional Imaging of Learning-Induced Plasticity in the Central Nervous System with Genetically Encoded Reporters in Drosophila.||Cold Spring Harb. Protoc.||[https://pubmed.ncbi.nlm.nih.gov/37197830  37197830 ]||[https://flybase.org/reports/FBrf0259620 FBrf0259620]
+|- bgcolor="lightgrey"
+| Protocol for Drosophila nervous system imaging.||Modeling neurodegenerative and neurodevelopmental disorders in the Drosophila mushroom body.||Learn. Mem.||[https://pubmed.ncbi.nlm.nih.gov/38876485  38876485 ]||[https://flybase.org/reports/FBrf0259776 FBrf0259776]
+|-
+| Extracellular superoxide dismutase 3 (SOD3) assay with whole ovaries.||Orthologs of NOX5 and EC-SOD/SOD3: dNox and dSod3 Impact Egg Hardening Process and Egg Laying in Reproductive Function of Drosophila melanogaster.||Int. J. Mol. Sci.||[https://pubmed.ncbi.nlm.nih.gov/38892326  38892326 ]||[https://flybase.org/reports/FBrf0259794 FBrf0259794]
+|- bgcolor="lightgrey"
+|}
+==== May 2024====
+{| class="wikitable"
+|-
+! ''Author description of technical advance''!!''Title''!!''Journal''!!''PubMed ID''!! ''FBrf number''
+|-
+| We have used the SBF-SEM to visualize the organelle contacts. ||ATF4-dependent increase in mitochondrial-endoplasmic reticulum tethering following OPA1 deletion in skeletal muscle.||J. Cell. Physiol.||[https://pubmed.ncbi.nlm.nih.gov/38419397  38419397 ]||[https://flybase.org/reports/FBrf0259269 FBrf0259269]
+|- bgcolor="lightgrey"
+| A transgenic chromatin interaction peptide-fused Cas9 exhibits higher mutagenesis efficiency. Additionally, a collection of UAS-sgRNAs transgenic flies have been shown to be valuable for chromoconnectome gene manipulation.||Conditional chemoconnectomics (cCCTomics) as a strategy for efficient and conditional targeting of chemical transmission.||eLife||[https://pubmed.ncbi.nlm.nih.gov/38686992  38686992 ]||[https://flybase.org/reports/FBrf0259397 FBrf0259397]
+|-
+| We established improved methods for collecting hemolymph and evaluating its osmolality more accurately and reproducibly.||Refinement of a technique for collecting and evaluating the osmolality of haemolymph from Drosophila larvae.||J. Exp. Biol.||[https://pubmed.ncbi.nlm.nih.gov/38634259  38634259 ]||[https://flybase.org/reports/FBrf0259426 FBrf0259426]
+|- bgcolor="lightgrey"
+| We created a suite of new DSCP-based reporter vectors for diverse insect species, leveraging dual compatibility with piggyBac and PhiC31-integration, the 3xP3 universal eye marker, GATEWAY cloning, different colors of reporters and markers, as well as Gal4-UAS binary expression.||A new suite of reporter vectors and a novel landing site survey system to study cis-regulatory elements in diverse insect species.||Sci. Rep.||[https://pubmed.ncbi.nlm.nih.gov/38698030  38698030 ]||[https://flybase.org/reports/FBrf0259440 FBrf0259440]
+|-
+| Resource: Drosophila adult eye proteome.||Eye proteome of Drosophila melanogaster.||Proteomics||[https://pubmed.ncbi.nlm.nih.gov/37963819  37963819 ]||[https://flybase.org/reports/FBrf0259492 FBrf0259492]
+|- bgcolor="lightgrey"
+| A new drosophila mutant with a loss of function mutation in the gene adipose. The previously used mutant adp[60] line is no longer available and this line adp[1] can replace it in functional studies as it phenocopies the increased fat storage.||A novel adipose loss-of-function mutant in Drosophila.||Fly||[https://pubmed.ncbi.nlm.nih.gov/38741287  38741287 ]||[https://flybase.org/reports/FBrf0259509 FBrf0259509]
+|-
+| This paper references the expression patterns of long non-coding RNAs available on the Fly-FISH database (link to database: https://fly-fish.ccbr.utoronto.ca/).||Spatially revealed roles for lncRNAs in Drosophila spermatogenesis, Y chromosome function and evolution.||Nat. Commun.||[https://pubmed.ncbi.nlm.nih.gov/38714658  38714658 ]||[https://flybase.org/reports/FBrf0259500 FBrf0259500]
+|- bgcolor="lightgrey"
+| It is a new resource.||Embryonic spatiotemporal expression pattern of Folded gastrulation suggests roles in multiple morphogenetic events and regulation by AbdA.||G3 (Bethesda)||[https://pubmed.ncbi.nlm.nih.gov/38366558  38366558 ]||[https://flybase.org/reports/FBrf0259445 FBrf0259445]
+|-
+| A set of IDR alignments across 33 Drosophila genomes where biochemical features of those IDRs have been scored for conservation using models of trait evolution||Evolutionary analyses of intrinsically disordered regions reveal widespread signals of conservation.||PLoS Comput. Biol.||[https://pubmed.ncbi.nlm.nih.gov/38662765  38662765 ]||[https://flybase.org/reports/FBrf0259452 FBrf0259452]
+|- bgcolor="lightgrey"
+|}
+==== Apr 2024====
+{| class="wikitable"
+|-
+! ''Author description of technical advance''!!''Title''!!''Journal''!!''PubMed ID''!! ''FBrf number''
+|-
+| Set of 52 genes were discovered in the paper that interact genetically with rdgB.||A genetic screen to uncover mechanisms underlying lipid transfer protein function at membrane contact sites.||Life Sci Alliance||[https://pubmed.ncbi.nlm.nih.gov/38499328  38499328 ]||[https://flybase.org/reports/FBrf0259024 FBrf0259024]
+|- bgcolor="lightgrey"
+| Method for building a device for administering time- and depth- calibrated closed-head injury to Drosophila.||dTBI2: A Calibrated, Tunable Device for Administering Traumatic Brain Injury in Drosophila.||Curr Protoc||[https://pubmed.ncbi.nlm.nih.gov/38511393  38511393 ]||[https://flybase.org/reports/FBrf0259091 FBrf0259091]
+|-
+| This is a protocol for the mass isolation of staged pupal intestines during Drosophila melanogaster development based on buoyancy in sucrose for biochemical evaluation of protein ubiquitylation. This protocol can be extended to investigate biochemical changes in other tissues.||Mass isolation of staged Drosophila pupal intestines for analysis of protein ubiquitylation.||STAR Protoc||[https://pubmed.ncbi.nlm.nih.gov/37950865  37950865 ]||[https://flybase.org/reports/FBrf0258960 FBrf0258960]
+|- bgcolor="lightgrey"
+| Automatic system for recognizing fly courtship.||An automatic system for recognizing fly courtship patterns via an image processing method.||Behav Brain Funct||[https://pubmed.ncbi.nlm.nih.gov/38493127  38493127 ]||[https://flybase.org/reports/FBrf0259038 FBrf0259038]
+|-
+| Ex-vivo live imaging of Drosophila pupal midgut intestianl stem cell divisions.||A live-imaging protocol for tracking intestinal stem cell divisions in the Drosophila melanogaster pupal midgut.||STAR Protoc||[https://pubmed.ncbi.nlm.nih.gov/38041821  38041821 ]||[https://flybase.org/reports/FBrf0258953 FBrf0258953]
+|- bgcolor="lightgrey"
+| This paper describes an automated robotic microinjection system for Drosophila and zebrafish.||High-throughput genetic manipulation of multicellular organisms using a machine-vision guided embryonic microinjection robot.||Genetics||[https://pubmed.ncbi.nlm.nih.gov/38373262  38373262 ]||[https://flybase.org/reports/FBrf0259210 FBrf0259210]
+|-
+| We have developed a tissue-specific O-GlcNAcylation profiling tool to enrich candidate substrates. Through this tool, we mapped the O-GlcNAc interactome and created an O-GlcNAc atlas for various brain regions of Drosophila (tsOGA, http://www.kyuanlab.com/tsOGA).||Tissue-specific O-GlcNAcylation profiling identifies substrates in translational machinery in Drosophila mushroom body contributing to olfactory learning.||eLife||[https://pubmed.ncbi.nlm.nih.gov/38619103  38619103 ]||[https://flybase.org/reports/FBrf0259241 FBrf0259241]
+|- bgcolor="lightgrey"
+| Split inteins are incorporated into Trojan-exon (Diao F et al, 2015) to make gene specific drivers.||Hox gene-specific cellular targeting using split intein Trojan exons.||Proc. Natl. Acad. Sci. U.S.A.||[https://pubmed.ncbi.nlm.nih.gov/38602904  38602904 ]||[https://flybase.org/reports/FBrf0259289 FBrf0259289]
+|-
+| A method to synchronise female germline stem cell differentiation in vivo, generating sufficient material for 'omics or biochemistry experiments at specified stages of differentiation. The study includes RNA-seq and Ribo-seq from this material, at 6 stages of differentiation.||Two distinct waves of transcriptome and translatome changes drive Drosophila germline stem cell differentiation.||EMBO J.||[https://pubmed.ncbi.nlm.nih.gov/38480936  38480936 ]||[https://flybase.org/reports/FBrf0259258 FBrf0259258]
+|- bgcolor="lightgrey"
+| The use of pseudo-time analysis in single-embryo RNA-sequencing data to determine developmental stage instead of manual embryo staging, thus avoiding human errors. Furthermore, we validated an approach to identify male and female embryos using their transcriptomes.||Single-embryo RNA sequencing for continuous and sex-specific gene expression analysis on Drosophila.||STAR Protoc||[https://pubmed.ncbi.nlm.nih.gov/37682716  37682716 ]||[https://flybase.org/reports/FBrf0258985 FBrf0258985]
+|-
+|}
+==== Mar 2024====
+{| class="wikitable"
+|-
+! ''Author description of technical advance''!!''Title''!!''Journal''!!''PubMed ID''!! ''FBrf number''
+|-
+| Single cell sequencing of pupal to adult midgut development. Provides information about cell types and genes expressed in these as the gut undergoes final adult maturation.||The emergence of circadian timekeeping in the intestine.||Nat. Commun.||[https://pubmed.ncbi.nlm.nih.gov/38413599  38413599 ]||[https://flybase.org/reports/FBrf0258833 FBrf0258833]
+|- bgcolor="lightgrey"
+| A transgene encoding a membrane-tethered form of Noktochor, a protein that is normally secreted from astrocytes and neurons to regulate sleep.||Drosophila noktochor regulates night sleep via a local mushroom body circuit.||iScience||[https://pubmed.ncbi.nlm.nih.gov/38380256  38380256 ]||[https://flybase.org/reports/FBrf0258837 FBrf0258837]
+|-
+| A collection of cell-type-specific  stable-split GAL4 reagents for courtship song neurons. https://splitgal4.janelia.org/precomputed/Lillvis%202023.html||Nested neural circuits generate distinct acoustic signals during Drosophila courtship.||Curr. Biol.||[https://pubmed.ncbi.nlm.nih.gov/38295797  38295797 ]||[https://flybase.org/reports/FBrf0258823 FBrf0258823]
+|- bgcolor="lightgrey"
+| A new drug stabilizable GAL80ds variant was created by fusing it to a low-background DHFR-22-DD.||A drug stabilizable GAL80[ds] for conditional control of gene expression via GAL4-UAS and CRISPR-Cas9 systems in Drosophila.||Sci. Rep.||[https://pubmed.ncbi.nlm.nih.gov/38467687  38467687 ]||[https://flybase.org/reports/FBrf0259011 FBrf0259011]
+|-
+| Transformer female-specific introns from three speices (D. melanogaster, D. suzukii, and C. capitata) were tested to show female-specificity at different developmental stages in D. melanogaster. This can be used for female-specific expression study.||A Fluorescent Sex-Sorting Technique for Insects with the Demonstration in Drosophila melanogaster.||GEN Biotechnol||[https://pubmed.ncbi.nlm.nih.gov/38415050  38415050 ]||[https://flybase.org/reports/FBrf0258926 FBrf0258926]
+|- bgcolor="lightgrey"
+| We generated a tool kit to express each Zika virus protein in Drosophila.||A Zika virus protein expression screen in Drosophila to investigate targeted host pathways during development.||Dis. Model Mech.||[https://pubmed.ncbi.nlm.nih.gov/38214058  38214058 ]||[https://flybase.org/reports/FBrf0258902 FBrf0258902]
+|-
+| A protocol for studying the neural circuit of female receptivity in Drosophila.||A protocol for measuring the sexual receptivity of female Drosophila.||STAR Protoc||[https://pubmed.ncbi.nlm.nih.gov/37703181  37703181 ]||[https://flybase.org/reports/FBrf0259009 FBrf0259009]
+|- bgcolor="lightgrey"
+| We have developed a glyoxal-based fast fixation method for IF, FISH and FISH-IF in Drosophila embryos. We also show that some antibodies like Bic-D, Dynein Heavy Chain and a-Actinin that failed to stain in formaldehyde fixed embryos, were stained beautifully with glyoxal fixation||Glyoxal-based fixation of Drosophila embryos for immunofluorescence staining and RNA in situ hybridization.||STAR Protoc||[https://pubmed.ncbi.nlm.nih.gov/37405926  37405926 ]||[https://flybase.org/reports/FBrf0258995 FBrf0258995]
+|-
+| New Ca2+ imaging probes targets to subcellular compartments. ||Ca[2+] imaging of synaptic compartments using subcellularly targeted GCaMP8f in Drosophila.||STAR Protoc||[https://pubmed.ncbi.nlm.nih.gov/38198278  38198278 ]||[https://flybase.org/reports/FBrf0259069 FBrf0259069]
+|- bgcolor="lightgrey"
+|}
 ==== Feb 2024====
@@ Line 44: / Line 260: @@
 | Advanced light sheet microscopy technique based on convolutional neural networks to augment live-imaging data with deep-tissue images taken on fixed samples.||Image restoration of degraded time-lapse microscopy data mediated by near-infrared imaging.||Nat. Methods||[https://pubmed.ncbi.nlm.nih.gov/38177507  38177507 ]||[https://flybase.org/reports/FBrf0258736 FBrf0258736]
 |- bgcolor="lightgrey"
-| A method called DISSECT, for DisPerSE (Discrete Persistent Structure Extractor)-based Segmentation and Exploration of Cells and Tissues, that offers the opportunity to extract automatically, in strongly deformed epithelia, a precise characterization of the spatial organization of a given cytoskeletal network combined with morphological quantifications in highly remodeled three-dimensional (3D) epithelial tissues is described.||DISSECT is a tool to segment and explore cell and tissue mechanics in highly deformed 3D epithelia.||Dev. Cell||[https://pubmed.ncbi.nlm.nih.gov/37586367  37586367 ]||[https://flybase.org/reports/FBrf0257870 FBrf0257870]
+| A method called DISSECT offers the opportunity to extract automatically, in strongly deformed epithelia, a precise characterization of the spatial organization of a given cytoskeletal network combined with morphological quantifications in highly remodeled three-dimensional (3D) epithelial tissues.||DISSECT is a tool to segment and explore cell and tissue mechanics in highly deformed 3D epithelia.||Dev. Cell||[https://pubmed.ncbi.nlm.nih.gov/37586367  37586367 ]||[https://flybase.org/reports/FBrf0257870 FBrf0257870]
 |}

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