FlyBase:Papers with technical advances

Papers of interest

Overview

This page lists potential papers of interest. Authors of these papers suggest that they include a technical advance, new type of reagent, or resource likely to be useful for other researchers. We started collecting author suggestions for papers in October 2020; these are listed below, with the most recent papers at the top. Please note, there will be a lag time before listed papers can be found on FlyBase and the submission date does not necessarily match the publication date of the paper.

Papers

December 2020

FBrf number	PubMed ID	Journal	Title	Author description
FBrf0247159	32917721	G3 (Bethesda)	Analysis of Gal4 Expression Patterns in Adult Drosophila Females.	Analysis of Gal4 expression patterns of commonly used Gal4 drivers in adult females.
FBrf0247182	33060173	Genome Res.	Active retrotransposons help maintain pericentromeric heterochromatin required for faithful cell division.	We defined the origins of repeat-derived RNAs and their specific chromatin locations in Drosophila S2 cells using the global RNA–DNA interaction sequencing method(GRID-seq).
FBrf0247192	33168136	eLife	The Drosophila Individual Activity Monitoring and Detection System (DIAMonDS).	We have developed a novel automated Drosophila life cycle multi-phase transition (pupariation, eclosion, and death) timing detection and measurement system with high accuracy and high temporal resolution.
FBrf0247218	33176146	Cell Rep.	Intramacrophage ROS Primes the Innate Immune System via JAK/STAT and Toll Activation.	A hydrogen peroxide probe was detected in vivo through a burnt fluorescent probe (TCFB, 2-Dicyanomethylene-3-cyano-4,5,5-trimethyl-2,5-dihydrofuran) [Sedgwick et al., 2017].
FBrf0247316	33113043	Apoptosis	Functional characterization of the Drosophila suzukii pro-apoptotic genes reaper, head involution defective and grim.	The binary expression of different pro-apoptotic genes using 2A peptides.
FBrf0247326	33016195	Fly	A pipeline for precise and efficient genome editing by sgRNA-Cas9 RNPs in Drosophila.	Improved pipeline for CRISPR mediated genome editing in Drosophila species. Generation of new vector to make donor plasmids for homology-directed repair
FBrf0247327	33234068	Open Biol.	The application of rapid evaporative ionization mass spectrometry in the analysis of Drosophila species-a potential new tool in entomology.	We describe a novel high throughput mass spectrometry approach to identifying species and sex by their metabolites. We show it works invertebrates generally, and can accurately distinguish closely related Drosophila (e.g. melanogaster and simulans) with potential for mass scoring
FBrf0247119	32973040	Genome Res.	Transposon expression in the Drosophila brain is driven by neighboring genes and diversifies the neural transcriptome.	Here we introduce TEchim, a new software that extracts chimeric sequencing reads that span transposon-gene breakpoints. In addition, we introduce scHardyWeinberg, a new approach to quantify co-expression levels in high-throughput single-cell sequencing data.
FBrf0247148	33159074	Nat. Commun.	A single-cell atlas and lineage analysis of the adult Drosophila ovary.	Single-cell RNA-sequencing dataset of the adult Drosophila ovary containing transcriptome profiles for all major ovarian cell types.
FBrf0247254	33184447	Commun. Biol.	A sensitive mNeonGreen reporter system to measure transcriptional dynamics in Drosophila development.	We developed an optimized version of the bright and fast-maturing fluorescent protein mNeonGreen to serve as a real-time, quantitative reporter of gene/enhancer expression.
FBrf0247413	33274326	Micropub Biol	Evidence of slightly increased Pol II pausing in UPF1-depleted Drosophila melanogaster cells.	DRB treatment followed by Pol II ChIP

November 2020

FBrf number PubMed ID Journal Title Author description

FBrf0246918 32955431 eLife AANAT1 functions in astrocytes to regulate sleep homeostasis. Antibody

FBrf0246897 33036271 Biomedicines Humanization of Drosophila Gαo to Model GNAO1 Paediatric Encephalopathies. Endogenous locus was edited with a two-step CRISPR/Cas9-mediated replacement.

FBrf0246907 32917765 Biol. Open Quantifying Drosophila adults with the use of a smartphone. We optimized, tested, and introduced a new method of automated count of Drosophila adults using the SeedCounter mobile application. The application is available on all mobile devices based on the Android system, and it does not require any additional equipment.

FBrf0246919 32783958 J. Insect Physiol. How to use the development of individual Drosophila larvae as a metabolic sensor. We introduce a developmental 96-well plate assay to use individual Drosophila larvae as tool for metabolic studies.

FBrf0247073 33077914 Nat. Genet. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Novel method to compare 3D chromatin conformation data in Drosophila

FBrf0247109 32814018 Neuron Synthesis of Conserved Odor Object Representations in a Random, Divergent-Convergent Network. Comprehensive calcium imaging from all 2,000 Kenyon cells in the mushroom body at single cell resolution.

FBrf0247160 33155978 eLife Modulation of flight and feeding behaviours requires presynaptic IP3Rs in dopaminergic neurons. Dominant negative form of IP3R protein. It has three mutated amino acids which prevent ligand binding. IP3R being tetramer, requires IP3 binding to all monomers. Hence presence of even single IP3R-DN monomer in tetramer can render whole IP3R protein complex functionless.

FBrf0247169 32916115 Curr. Biol. Collective Cell Sorting Requires Contractile Cortical Waves in Germline Cells. use of Hydrogel for live-imaging of Drosophila ovaries

FBrf0247175 33048531 Anal. Chem. Real-Time Measurement of Stimulated Dopamine Release in Compartments of the Adult Drosophila melanogaster Mushroom Body. This paper uses fast-scan cyclic voltammetry at a carbon-fiber microelectrode to make real-time measurement of stimulated endogenous dopamine release in the mushroom body of adult Drosophila brains using various stimulation techniques

FBrf0247184 33163946 iScience Transcription Factor Binding Affinities and DNA Shape Readout. New measurements of Position weight Matrices (PWMs) Dinucleotide Position weight Matrices (DPWMs) for 13 Drosophila transcription factors and their DNA shape analysis for all shape features.

FBrf0247019 33108408 PLoS ONE Three distinct mechanisms, Notch instructive, permissive, and independent, regulate the expression of two different pericardial genes to specify cardiac cell subtypes. Sequence, features, and schematic of the pWattB-nlacZ reporter construct vector

FBrf0247101 33117817 Front. Cell Dev. Biol. An Immobilization Technique for Long-Term Time-Lapse Imaging of Explanted Drosophila Tissues. A new method for immobilizing explanted Drosophila tissue in agarose for use in long-term live imaging.

FBrf0247149 32955048 Analyst Improving serotonin fast-scan cyclic voltammetry detection: new waveforms to reduce electrode fouling. Using new fast-scan cyclic voltammetry serotonin specific waveforms for in vivo detection of serotonin in Drosophila tissue.

FBrf0247179 33090988 PLoS Biol. Interphase-arrested Drosophila embryos activate zygotic gene expression and initiate mid-blastula transition events at a low nuclear-cytoplasmic ratio. We have developed a new protocol to indcue cell cycle arrest in early embryos, and deposited RNA-seq data for WT embryos and embryos arrested in cycle 12 for differernt amount of time.

FBrf0247228 31960114 Cell. Molec. Life Sci. Loss of function in the Drosophila clock gene period results in altered intermediary lipid metabolism and increased susceptibility to starvation. Analysis of the chronometabolome including lipids

FBrf0247230 33177090 Sci. Adv. Persistent epigenetic reprogramming of sweet taste by diet. Transgenic Targeted DamID construct for the gene polycomb-like (Pcl) under the control of a UAS.

October 2020

FBrf number PubMed ID Journal Title Author description

FBrf0246799 32013401 Biochemistry Subverting Hedgehog Protein Autoprocessing by Chemical Induction of Paracatalysis. Small molecules called "HACs" alter normal autoprocessing activity of hedgehog precursor protein. Instead of reacting with cholesterol (cholesterolysis), the HACs alter hedgehog precursor autoprocessing toward a side reaction with water (hydrolysis).'

FBrf0246922 32901612 eLife Topology-driven protein-protein interaction network analysis detects genetic sub-networks regulating reproductive capacity. This paper shows how computational network analyses based on protein-protein interactions can be used to augment genetic screens to identify genes involved in essential developmental processes. The code are deposited in GitHub https://github.com/extavourlab/hpo_ova_eggL_screen.

FBrf0246250 32652492 iScience PhotoGal4: A Versatile Light-Dependent Switch for Spatiotemporal Control of Gene Expression in Drosophila Explants. PhotoGal4 is a phytochrome B-based optogenetic switch for fine tuned spatiotemporal control of gene expression in Drosophila explants. PhotoGal4 activates and deactivates gene expression upon red- or far-red-light irradiation.

FBrf0246808 32973185 Sci. Rep. A novel setup for simultaneous two-photon functional imaging and precise spectral and spatial visual stimulation in Drosophila. We developed a unique visual stimulation setup to probe spectral, spatial, & temporal properties using neural activity imaging. Custom optical filters enabled simultaneous two-photon imaging & visual stimulation over a wide range of hues without compromising the temporal rates.

FBrf0246889 32745561 J. Insect Physiol. CRISPR/Cas9 mediated disruption of the white gene leads to pigmentation deficiency and copulation failure in Drosophila suzukii. New white gene mutant strains were generated in Drosophila suzukii and can be used as resources to study the corresponding phenotype.

FBrf0246845 32958931 Nat. Protoc. CRISPR-based engineering of gene knockout cells by homology-directed insertion in polyploid Drosophila S2R+ cells. This protocol allows generation of homozygous mutant cell lines using an insertion cassette which autocatalytically generates insertion mutations in all alleles. Knockout cells generated using this method can be directly identified by PCR without a need for DNA sequencing.

FBrf0246864 32759315 J. Virol. Partitiviruses Infecting Drosophila melanogaster and Aedes aegypti Exhibit Efficient Biparental Vertical Transmission. Drosophila melanogaster line infected only with galbut virus (FoCo-17 line 30).

FBrf0246967 33064752 PLoS ONE Comparative proteomics analysis of dietary restriction in Drosophila. The isobaric tags for relative and absolute quantification (iTRAQ) technology was chosen to sequence the proteomes of Drosophila.