Log In Sign up
The largest database of trusted experimental protocols
> Living Beings > Eukaryote > Drosophila

Drosophila

Drosophila, also known as the fruit fly, is a genus of small flies that are widely used as a model organism in biological research.
These insects have a short life cycle, are easy to maintain in the laboratory, and have a well-characterized genome, making them a valuable tool for studying genetics, development, behavior, and disease.
Drosophila are particularly useful for investigating topics such as cell signaling pathways, neural development, and the genetic basis of complex traits.
Researchers in fields like genetics, neuroscience, and developmental biology often utilize Drosophila to gain insights that can be applied to other organisms, including humans.
With their versatility and wealth of available data, Drosophila continue to be an indispensible model for advancing our understanding of fundamental biological processes.

Most cited protocols related to «Drosophila»

1
Probabilistic Modeling for Accurate Gene Prediction
Cited 476 times
AUGUSTUS is based on a generalized hidden Markov model (GHMM), which defines probability distributions for the various sections of genomic sequences. Introns, exons, intergenic regions, etc. correspond to states in the model and each state is thought to create DNA sequences with certain pre-defined emission probabilities. Similar to other HMM-based gene finders, AUGUSTUS finds an optimal parse of a given genomic sequence, i.e. a segmentation of the sequences into states that is most likely according to the underlying statistical model. We probabilistically model the sequence around the splice sites, the sequence of the branch point region, the bases before the translation start, the coding regions and non-coding regions, the first coding bases of a gene, the length distribution of single exons, initial exons, internal exons, terminal exons, intergenic regions, the distribution of the number of exons per gene and the length distribution of introns.
The performance of AUGUSTUS has been extensively evaluated on sequence data from human and Drosophila (7 ,8 (link)) (). These studies showed that, especially for long input sequences, the accuracy of our program is superior to that of existing ab initio gene finding approaches. To make our tool available to the research community, we have set up a WWW server at GOBICS (Göttingen Bioinformatics Compute Server) (9 (link)).
AUGUSTUS may be forced to predict an exon, an intron, a splice site, a translation start or a translation end point at a certain position in the sequence. An arbitrary number of such constraints is allowed and supported types of constraints are given in Table 1.
With the term gene structure, we refer to a segmentation of the input sequence into any meaningful sequence of exons, introns and intergenic regions. This includes the possibility of having no genes at all or of having multiple genes. AUGUSTUS tries to predict a gene structure that

is (biologically) consistent in the following sense:

No exon contains an in-frame stop codon.

The splice sites obey the gt–ag consensus. All complete genes start with atg and end with a stop codon.

Each gene ends before the next gene starts.

The lengths of single exons and introns exceed a species-dependent minimal length.

That obeys all given constraints.

Among all gene structures that are consistent and that obey all constraints, AUGUSTUS finds the most likely gene structure. A constraint may contradict the biological consistency. For example, an exonpart constraint may be impossible to realize because there is no containing open reading frame with allowed exon boundaries. If no consistent gene structure is possible, which obeys all constraints, then some constraints are ignored. Also, if two or more constraints contradict each other, then AUGUSTUS obeys only that constraint that fits better to the model. Figure 1 illustrates the concept. Further examples are on the page .
Stanke M, & Morgenstern B. (2005). AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Research, 33(Web Server issue), W465-W467.
Publication 2005
Biopharmaceuticals Codon, Terminator Drosophila Exons Genes Genetic Structures Genome Homo sapiens Intergenic Region Introns Multiple Birth Offspring Reading Frames Seizures
2
CRISPR-Cas9 Genome Editing in Cells
Cited 336 times
For human cells, expression vector PX330 (Addgene plasmid 42230) encoding Cas9 and chimeric guide RNA was used (11 (link)). The LBR guides were cloned into expression vector pBluescript with the sgRNA cassette of PX330 and transfected into the K562 line stably transformed with Cas9. For Drosophila cells, Cas9 expression vector pBS-Hsp70-Cas9 (Addgene plasmid 46294) was used in combination with pU6-BbsI-chiRNA construct (Addgene plasmid 45946) (12 (link)). The sgRNAs were designed using CRISPR design (http://crispr.mit.edu/) (13 (link)) and CHOPCHOP (https://chopchop.rc.fas.harvard.edu/) (14 (link)).
The following sgRNA sequences were used:
For the cloning of individual DNA fragments from the edited GFP gene, PCR products were ligated in Zero Blunt vector (Invitrogen) using standard procedures.
Brinkman E.K., Chen T., Amendola M, & van Steensel B. (2014). Easy quantitative assessment of genome editing by sequence trace decomposition. Nucleic Acids Research, 42(22), e168.
Full text: Click here
Publication 2014
Cells Chimera Cloning Vectors Clustered Regularly Interspaced Short Palindromic Repeats Drosophila Genes Heat-Shock Proteins 70 Homo sapiens Plasmids
3
Drosophila Genome Analysis Pipeline
Cited 297 times
Image analysis software was provided as part of the Genome Analyzer analysis pipeline and configured for fully automatic parameter selection. Single-end reads were 76 bases in total length. Quality control was performed using FastQC, showing overall low error rates. The reference genome used was the latest FlyBase version at the time (y1; cn1bw1sp1 strain, Dm5.30). The data was aligned using the BWA algorithm (Li and Durbin, 2009 (link)). A total of 5,234,506 reads were NOT mapped to the genome (i.e., 10.01%). This is usually due to low quality reads or reads have missing base calling information (i.e., “B” in the quality stream). The rest of the reads for X1 and X2 were mapped as indicated. Gap estimation: according to the mapping software, the gap between pair-end reads is 360 ± 20 bp. The distribution percentiles are 345 (25%), 360 (50%), and 375 (75%). The set of6 and to the NCBI’s map of RefSeq and candidate Drosophila genes7.
Reads were filtered using a minimum mapping quality of 20 (MAPQ). Variant calling was performed using SamTools (Li et al., 2009 (link)) and BcfTools. When using individual calls without base alignment quality (BAQ) model, (Li, 2011 (link)) a total of 1,036,435 homozygous SNPs were detected. Using multi-sample calling methods and BAQ model, (Li, 2011 (link)) the number of homozygous SNPs was reduced to 204,250. Variant annotation and filtering was performed using the software SnpEff (Cingolani et al., Fly, in press) and SnpSift, described below.
Cingolani P., Patel V.M., Coon M., Nguyen T., Land S.J., Ruden D.M, & Lu X. (2012). Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift. Frontiers in Genetics, 3, 35.
Publication 2012
A 435 Drosophila Genome Homozygote Single Nucleotide Polymorphism
4
Compilation of Reference Protein Sets
Cited 188 times
The protein sets for all newly included bacterial and archaeal genomes, the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, the microsporidian Encaephalitozoon cuniculi, the thale cress Arabidopsis thaliana, and the fruit fly Drosophila melanogaster were extracted from the Genome division of the (NCBI, NIH, Bethesda). The protein sequences for the nematode Caenorhabditis elegans were from the WormPep67 database, the sequences for Homo sapiens were from the NCBI build 30.
Tatusov R.L., Fedorova N.D., Jackson J.D., Jacobs A.R., Kiryutin B., Koonin E.V., Krylov D.M., Mazumder R., Mekhedov S.L., Nikolskaya A.N., Rao B.S., Smirnov S., Sverdlov A.V., Vasudevan S., Wolf Y.I., Yin J.J, & Natale D.A. (2003). The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 4, 41.
Publication 2003
Amino Acid Sequence Arabidopsis thalianas Bacteria Caenorhabditis elegans Cuniculus Drosophila Drosophila melanogaster Genome Genome, Archaeal Homo sapiens Microspora Nematoda Proteins Saccharomyces cerevisiae Schizosaccharomyces pombe Yeasts
5
TrakEM2 for Drosophila Neuropil Analysis
Cited 143 times
The EM data used here to exemplify the use of TrakEM2 corresponds to the abdominal neuropil of the first instar larva of Drosophila, and will be made available in full elsewhere.
Cardona A., Saalfeld S., Schindelin J., Arganda-Carreras I., Preibisch S., Longair M., Tomancak P., Hartenstein V, & Douglas R.J. (2012). TrakEM2 Software for Neural Circuit Reconstruction. PLoS ONE, 7(6), e38011.
Full text: Click here
Publication 2012
Abdomen Drosophila Larva Neuropil

Most recents protocols related to «Drosophila»

1
Drosophila Antimonyl Tartrate Exposure
Potassium antimonyl tartrate trihydrate (C8H4K2O12Sb2·3H2O, 99.0–103%; Sigma-Aldrich, St. Louis, MO, USA) was used in this study. Three different environmental exposures of Sb with relevant final concentrations (0.3, 0.6, and 1.2 mg/mL) were chosen. Two- to three-day-old male flies of the W1118 line were then placed in standard Drosophila food medium containing Sb for 10 days (referred as the chemical exposed group). Control male W1118 flies were placed in standard Drosophila food medium without Sb for 10 days.
Yu J., Fu Y., Li Z., Huang Q., Tang J., Sun C., Zhou P., He L., Sun F., Cheng X., Ji L., Yu H., Shi Y., Gu Z., Sun F, & Zhao X. (2023). Single-cell RNA sequencing reveals cell landscape following antimony exposure during spermatogenesis in Drosophila testes. Cell Death Discovery, 9, 86.
Full text: Click here
Publication 2023
Diptera Drosophila Environmental Exposure Food Males potassium tartrate
2
Drosophila Fly Stocks and Rearing Protocol
The Drosophila melanogaster Oregon R (modENCODE, FBst0025211) and Phs-hidY (FBst0024638; Grether et al. 1995 (link)) fly stocks were obtained from the Bloomington Drosophila Stock center (Cook et al. 2010 (link)). The Drosophila melanogaster Canton S flies were obtained from the Bloomington Drosophila Stock center (RRID:BDSC_64349). Flies were grown on either Cornmeal, Sucrose, and Yeast Media (LabExpress fly media) or Glucose, Active Yeast, and proprionic acid media (10:5 fly media) at 25 ∘ C, 60% RH. 5 females and 4 males were placed per vial for Oregon R and approximately 10 female and male flies per vial for Canton S. Oregon R flies were transferred to fresh vials daily and progeny from previous vials were collected for experiments. Canton S flies were transferred to fresh vials every 3–4 days and progeny were selected for experiments. An Oregon R stock with a Y chromosome carrying a Phs-hid insertion was generated (http://flystocks.bio.indiana.edu/Browse/misc-browse/hs-hid˙method.html), by crossing double balancer females with Y-lethal males crossed with Y-lethal males (FBst0024638, Grether et al. 1995 (link)). We introduced the Y chromosome into the Oregon R background using double balanced 2nd and 3rd chromosomes. The 4th chromosome was not tracked. For our experiments we used Oregon R (FBst0025211) males and virgin females obtained from the Oregon R Y-lethal stock after 37 ∘ C heat shock using a water bath for 2 h during third instar. Canton S flies sex were sorted after mating, for female only experimentation. We verified the absence of males during collection of individual flies. When males were present in the vial, none of those flies were used for experiments. This occurred in about 1 out of every 10 heat shocked vials. Newly enclosed flies were placed in batches of 35 per vial for use in experimental assays. Vials contained either CDF (Lee and Micchelli 2013 (link)), LabExpress fly media, or 10:5 fly media . Flies were aged for 3–4 days at 25 ∘ C 60% RH. After aging on solid food, flies were loaded in the WAFFL (as described below) to proceed with the defined assays.
Jaime M.D., Salem G.H., Martinez D.J., Karott S., Flores A., Palmer C.D., Mahadevaraju S., Krynitsky J., Garmendia-Cedillos M., Anderson S., Harbison S., Pohida T.J., Ludington W.B, & Oliver B. (2023). Whole Animal Feeding FLat (WAFFL): a complete and comprehensive validation of a novel, high-throughput fly experimentation system. G3: Genes|Genomes|Genetics, 13(3), jkad012.
Full text: Click here
Publication 2023
Acids Bath Biological Assay Chromosomes Diptera Drosophila Drosophila melanogaster Females Food Glucose Heat-Shock Response Males Sucrose Y Chromosome Yeast, Dried
3
Detecting Dominant Lethal Mutations in Fruit Flies

Protocol full text hidden due to copyright restrictions

Open the protocol to access the free full text link

Publication 2023
Agar carvacrol carvone Culture Media Diptera Drosophila Eggs Embryo Embryo Death Females Males Mutation Thymol
4
Unbiased Genetic Modifier Screen for CMT
We chose to screen for EP lines on the Drosophila X-chromosome as a strategy to identify YARS1CMT-relevant genetic interactions in an unbiased manner, and yet avoid a lengthy whole-genome screening, or screening for EP lines of the much larger chromosomes 2 or 3. The screening was performed as described in ref. 39 (link). Briefly, GMR-Gal4; UAS-YARS1E196K/TM6B virgins were crossed with EP males. In case of EP male sterility or lethal EP-element insertion, crosses were repeated vice versa, using EP virgins and GMR-Gal4; UAS-YARS1E196K/TM6B males. In F1, at least 20 female flies heterozygous for GMR-Gal>YARS1E196K>EP and GMR-Gal4>TM6B>EP genotypes were compared with each other. Initial positive hits were selected when rough eye phenotype was present in flies with the first genotype and was absent in flies with the second genotype, respectively. The crosses for the positive hits were repeated at least three independent times. In a next step, the initially positive hit went through a rigorous validation process, where the major criterium to be claimed as a genuine CMT modifier was to induce a rough-eye phenotype only upon co-expression with YARS1E196K and not with YARS1WT. Additionally, the genetic interaction had to be evolutionary conserved (i.e., present both with human and Drosophila versions of YARS1E196K) (see Fig. 1a for a schematic representation of the screening strategy).
Ermanoska B., Asselbergh B., Morant L., Petrovic-Erfurth M.L., Hosseinibarkooie S., Leitão-Gonçalves R., Almeida-Souza L., Bervoets S., Sun L., Lee L., Atkinson D., Khanghahi A., Tournev I., Callaerts P., Verstreken P., Yang X.L., Wirth B., Rodal A.A., Timmerman V., Goode B.L., Godenschwege T.A, & Jordanova A. (2023). Tyrosyl-tRNA synthetase has a noncanonical function in actin bundling. Nature Communications, 14, 999.
Full text: Click here
Publication 2023
Biological Evolution Chromosomes, Human, Pair 2 Diptera Drosophila Females Genome Genotype Heterozygote Homo sapiens Males Muscle Rigidity Phenotype Reproduction X Chromosome
5
Drosophila Transgenic Protein Expression
All Drosophila crosses were performed at 25 °C, 12 h light/dark cycle, on a standard NutriFly medium (Flystuff). UAS-YARS1 flies, expressing full-length human (YARS1) and Drosophila (dYARS1) proteins, were previously described in ref. 15 (link). To generate UAS-YARS1::GFP transgenic flies, eGFP was inserted at the N-terminal of human YARS1WT or YARS1E196K in the pEGFPC1 vector, which was sub-cloned into the pUAST transformation vector. UAS-dGARS1 flies carrying the cytoplasmic isoform of the Drosophila orthologue of glycyl-tRNA synthetase (wild type and mutants) were previously reported in ref. 39 (link). All constructs were sequence verified and transgenic flies were generated using standard procedures. For each construct, multiple transgenic lines were established. All transgenic flies used are in the w1118 genetic background.
Ermanoska B., Asselbergh B., Morant L., Petrovic-Erfurth M.L., Hosseinibarkooie S., Leitão-Gonçalves R., Almeida-Souza L., Bervoets S., Sun L., Lee L., Atkinson D., Khanghahi A., Tournev I., Callaerts P., Verstreken P., Yang X.L., Wirth B., Rodal A.A., Timmerman V., Goode B.L., Godenschwege T.A, & Jordanova A. (2023). Tyrosyl-tRNA synthetase has a noncanonical function in actin bundling. Nature Communications, 14, 999.
Full text: Click here
Publication 2023
Animals, Transgenic Cloning Vectors Cytoplasm Diptera Drosophila Genetic Background Glycine-tRNA Ligase Homo sapiens Protein Isoforms Proteins

Top products related to «Drosophila»

1
Schneider s drosophila medium by Thermo Fisher Scientific
Sourced in United States, United Kingdom, France, China
Schneider's Drosophila medium is a specialized cell culture medium designed for the growth and maintenance of Drosophila cell lines. It provides the essential nutrients and growth factors required for the optimal cultivation of these insect-derived cells.
2
Fetal bovine serum (fbs) by Thermo Fisher Scientific
Sourced in United States, China, United Kingdom, Germany, Australia, Japan, Canada, Italy, France, Switzerland, New Zealand, Brazil, Belgium, India, Spain, Israel, Austria, Poland, Ireland, Sweden, Macao, Netherlands, Denmark, Cameroon, Singapore, Portugal, Argentina, Holy See (Vatican City State), Morocco, Uruguay, Mexico, Thailand, Sao Tome and Principe, Hungary, Panama, Hong Kong, Norway, United Arab Emirates, Czechia, Russian Federation, Chile, Moldova, Republic of, Gabon, Palestine, State of, Saudi Arabia, Senegal
Fetal Bovine Serum (FBS) is a cell culture supplement derived from the blood of bovine fetuses. FBS provides a source of proteins, growth factors, and other components that support the growth and maintenance of various cell types in in vitro cell culture applications.
3
Penicillin streptomycin by Thermo Fisher Scientific
Sourced in United States, Germany, United Kingdom, China, Canada, France, Japan, Australia, Switzerland, Israel, Italy, Belgium, Austria, Spain, Gabon, Ireland, New Zealand, Sweden, Netherlands, Denmark, Brazil, Macao, India, Singapore, Poland, Argentina, Cameroon, Uruguay, Morocco, Panama, Colombia, Holy See (Vatican City State), Hungary, Norway, Portugal, Mexico, Thailand, Palestine, State of, Finland, Moldova, Republic of, Jamaica, Czechia
Penicillin/streptomycin is a commonly used antibiotic solution for cell culture applications. It contains a combination of penicillin and streptomycin, which are broad-spectrum antibiotics that inhibit the growth of both Gram-positive and Gram-negative bacteria.
4
W1118 by Bloomington Drosophila Stock Center
Sourced in United States
W1118 is a wild-type Drosophila melanogaster strain commonly used as a genetic background. It serves as a standard reference strain for various experimental studies in the field of Drosophila research.
5
Elav gal4 by Bloomington Drosophila Stock Center
Sourced in United States, United Kingdom
The Elav-Gal4 is a genetic tool used in Drosophila research. It is a driver line that expresses the Gal4 transcription factor under the control of the elav (embryonic lethal abnormal vision) gene promoter, which is active in all post-mitotic neurons. This allows for the targeted expression of transgenes in the neuronal cells of Drosophila.
6
Drosophila activity monitoring system by Trikinetics
Sourced in United States
The Drosophila Activity Monitoring System is a laboratory equipment designed to track and record the locomotor activity of Drosophila flies. It provides objective and automated data on the movement patterns of these model organisms.
7
Effectene transfection reagent by Qiagen
Sourced in Germany, United States, Netherlands, Spain, Japan, China, United Kingdom, Singapore
Effectene Transfection Reagent is a lipid-based transfection reagent used for the efficient delivery of DNA, RNA, proteins, and other macromolecules into a variety of eukaryotic cell types. It is designed to facilitate the uptake and expression of these molecules in the target cells.
8
Effectene by Qiagen
Sourced in Germany, United States, United Kingdom, Spain, Netherlands, Switzerland, France
Effectene is a transfection reagent developed by Qiagen. It is designed to efficiently deliver DNA, RNA, or other molecules into eukaryotic cells for various research applications.
9
Trizol reagent by Thermo Fisher Scientific
Sourced in United States, China, Japan, Germany, United Kingdom, Canada, France, Italy, Australia, Spain, Switzerland, Netherlands, Belgium, Lithuania, Denmark, Singapore, New Zealand, India, Brazil, Argentina, Sweden, Norway, Austria, Poland, Finland, Israel, Hong Kong, Cameroon, Sao Tome and Principe, Macao, Taiwan, Province of China, Thailand
TRIzol reagent is a monophasic solution of phenol, guanidine isothiocyanate, and other proprietary components designed for the isolation of total RNA, DNA, and proteins from a variety of biological samples. The reagent maintains the integrity of the RNA while disrupting cells and dissolving cell components.
10
Trizol by Thermo Fisher Scientific
Sourced in United States, Germany, China, Japan, United Kingdom, Canada, France, Italy, Australia, Spain, Switzerland, Belgium, Denmark, Netherlands, India, Ireland, Lithuania, Singapore, Sweden, Norway, Austria, Brazil, Argentina, Hungary, Sao Tome and Principe, New Zealand, Hong Kong, Cameroon, Philippines
TRIzol is a monophasic solution of phenol and guanidine isothiocyanate that is used for the isolation of total RNA from various biological samples. It is a reagent designed to facilitate the disruption of cells and the subsequent isolation of RNA.

More about "Drosophila"

Drosophila, also known as the fruit fly, is a genus of small flies that are widely used as a model organism in biological research.
These insects have a short life cycle, are easy to maintain in the laboratory, and have a well-characterized genome, making them a valuable tool for studying genetics, development, behavior, and disease.
Drosophila are particularly useful for investigating topics such as cell signaling pathways, neural development, and the genetic basis of complex traits.
Researchers in fields like genetics, neuroscience, and developmental biology often utilize Drosophila to gain insights that can be applied to other organisms, including humans.
When working with Drosophila, researchers may use Schneider's Drosophila medium, a commonly used culture medium that supports the growth and maintenance of Drosophila cells.
Fetal bovine serum (FBS) and penicillin/streptomycin are often added to the medium to provide additional nutrients and prevent bacterial contamination.
The W1118 strain is a widely used Drosophila line that serves as a genetic background for various experiments.
Elav-Gal4 is a commonly used driver line that expresses the Gal4 transcription factor in neurons, allowing for targeted gene expression in the nervous system.
The Drosophila Activity Monitoring System is a tool used to measure and analyze the locomotor activity of flies, providing insights into their behavior and circadian rhythms.
Effectene Transfection Reagent, a lipid-based transfection agent, is often used to introduce DNA into Drosophila cells, facilitating gene expression studies and other genetic manipulations.
TRIzol reagent, on the other hand, is a versatile tool for extracting high-quality RNA from Drosophila samples, enabling various molecular biology techniques.
With their versatility and wealth of available data, Drosophila continue to be an indispensible model for advancing our understanding of fundamental biological processes.
Optimizing your Drosophila research with tools like PubCompare.ai can help enhance reproducibility and accuracy, ensuring your studies are efficient and reliable.