#Drosophila now returns >90,000 results at PubMed. Let the count down to >100,000 begin!!! — Stephanie Mohr (@smohrfly) June 24, 2015
Wednesday, June 24, 2015
Search with "Drosophila" now returns >90,000 results in PubMed!
"Genetic toolkit" for intronic MiMICs
Nagarkar-Jaiswal S, DeLuca SZ, Lee PT, Lin WW, Pan H, Zuo Z, Lv J, Spradling AC, Bellen HJ. A genetic toolkit for tagging intronic MiMIC containing genes. Elife. 2015 Jun 23;4. PMID: 26102525.
From the abstract: "... Here we describe a simple and reliable genetic strategy to tag genes/proteins that contain MiMIC insertions using an integrated exon encoding GFP flanked by FRT sequences. We document the efficiency and tag 60 mostly uncharacterized genes."
Study uses transcriptomics and in vivo RNAi follow-up to explore sleep
Tomita J, Ueno T, Mitsuyoshi M, Kume S, Kume K. The NMDA Receptor Promotes Sleep in the Fruit Fly, Drosophila melanogaster. PLoS One. 2015 May 29;10(5):e0128101. PMID: 26023770; PMCID: PMC4449117.
From the abstract: "... sleep is essential for learning and memory. Drosophila melanogaster has emerged as a novel model for studying sleep. ... we carried out a microarray analysis comparing mRNA expression in heads of fmn and control flies and found that 563 genes are differentially expressed. Next, using the pan-neuronal Gal4 driver elav-Gal4 and UAS-RNA interference (RNAi) to knockdown individual genes, we performed a functional screen. We found that knockdown of the NMDA type glutamate receptor channel gene (Nmdar1) (also known as dNR1) reduced sleep. ..."
From the abstract: "... sleep is essential for learning and memory. Drosophila melanogaster has emerged as a novel model for studying sleep. ... we carried out a microarray analysis comparing mRNA expression in heads of fmn and control flies and found that 563 genes are differentially expressed. Next, using the pan-neuronal Gal4 driver elav-Gal4 and UAS-RNA interference (RNAi) to knockdown individual genes, we performed a functional screen. We found that knockdown of the NMDA type glutamate receptor channel gene (Nmdar1) (also known as dNR1) reduced sleep. ..."
Caffeine, kinases and the Hippo pathway: cell-based fly RNAi screen with in vivo follow-up
Di Cara F, Maile TM, Parsons BD, Magico A, Basu S, Tapon N, King-Jones K. The Hippo pathway promotes cell survival in response to chemical stress. Cell Death Differ. 2015 Mar 13. PMID: 26021298.
From the abstract: "Cellular stress defense mechanisms have evolved to maintain homeostasis in response to a broad variety of environmental challenges. Stress signaling pathways activate multiple cellular programs that range from the activation of survival pathways to the initiation of cell death when cells are damaged beyond repair. To identify novel players acting in stress response pathways, we conducted a cell culture RNA interference (RNAi) screen using caffeine as a xenobiotic stress-inducing agent, as this compound is a well-established inducer of detoxification response pathways. Specifically, we examined how caffeine affects cell survival when Drosophila kinases and phosphatases were depleted via RNAi. Using this approach, we identified and validated 10 kinases and 4 phosphatases that are essential for cell survival under caffeine-induced stress both in cell culture and living flies. Remarkably, our screen yielded an enrichment of Hippo pathway components, indicating that this pathway regulates cellular stress responses. ... Our in vitro and in vivo loss-of-function data therefore implicate Hippo signaling in the transduction of cellular survival signals in response to chemical stress."
From the abstract: "Cellular stress defense mechanisms have evolved to maintain homeostasis in response to a broad variety of environmental challenges. Stress signaling pathways activate multiple cellular programs that range from the activation of survival pathways to the initiation of cell death when cells are damaged beyond repair. To identify novel players acting in stress response pathways, we conducted a cell culture RNA interference (RNAi) screen using caffeine as a xenobiotic stress-inducing agent, as this compound is a well-established inducer of detoxification response pathways. Specifically, we examined how caffeine affects cell survival when Drosophila kinases and phosphatases were depleted via RNAi. Using this approach, we identified and validated 10 kinases and 4 phosphatases that are essential for cell survival under caffeine-induced stress both in cell culture and living flies. Remarkably, our screen yielded an enrichment of Hippo pathway components, indicating that this pathway regulates cellular stress responses. ... Our in vitro and in vivo loss-of-function data therefore implicate Hippo signaling in the transduction of cellular survival signals in response to chemical stress."
Thursday, June 18, 2015
miRNA "sponge" fly stock resource
Fulga TA, McNeill EM, Binari R, Yelick J, Blanche A, Booker M, Steinkraus BR, Schnall-Levin M, Zhao Y, DeLuca T, Bejarano F, Han Z, Lai EC, Wall DP, Perrimon N, Van Vactor D. A transgenic resource for conditional competitive inhibition of conserved Drosophila microRNAs. Nat Commun. 2015 Jun 17;6:7279. PMID: 26081261.
From the abstract: "... Development of competitive inhibitor molecules such as miRNA sponges has allowed the community to address individual miRNA function in vivo. ... Here we offer a comprehensive library of 141 conditional miRNA sponges targeting well-conserved miRNAs in Drosophila. ..."
From the abstract: "... Development of competitive inhibitor molecules such as miRNA sponges has allowed the community to address individual miRNA function in vivo. ... Here we offer a comprehensive library of 141 conditional miRNA sponges targeting well-conserved miRNAs in Drosophila. ..."
Wednesday, June 17, 2015
Sneak peak for blog readers: Gene List Annotation for Drosophila (GLAD) at DRSC
For years the DRSC has been putting together gene lists, e.g. to build focused cell-based RNAi libraries like our kinases and phosphatases library.
We recently built an online tool, GLAD, to support search and view of the several gene lists put together by Hu et al. over the years. When possible, the lists are annotated with information regarding confidence. Some lists are based on biochemical function (e.g. kinases) and others are based on biological function (e.g. autophagy). Check it out!
A companion paper has been accepted by Journal of Genomics. I'll post when it's out.
At the online tool, you can suggest additions or changes to the list, or suggest relevant papers, so that we can improve the resource over time.
We have also made it possible for the community to quickly use a gene list to find relevant TRiP and other RNAi fly stocks in public collections.
See also related post on the complementary gene groups resource at FlyBase.
We recently built an online tool, GLAD, to support search and view of the several gene lists put together by Hu et al. over the years. When possible, the lists are annotated with information regarding confidence. Some lists are based on biochemical function (e.g. kinases) and others are based on biological function (e.g. autophagy). Check it out! A companion paper has been accepted by Journal of Genomics. I'll post when it's out.
At the online tool, you can suggest additions or changes to the list, or suggest relevant papers, so that we can improve the resource over time.
We have also made it possible for the community to quickly use a gene list to find relevant TRiP and other RNAi fly stocks in public collections.
See also related post on the complementary gene groups resource at FlyBase.
C. elegans study points to pol theta involvement in CRISPR mediated events
From our worm colleagues--article of possible interest to folks working with CRISPR system:
van Schendel R, Roerink SF, Portegijs V, van den Heuvel S, Tijsterman M. Polymerase Θ is a key driver of genome evolution and of CRISPR/Cas9-mediated mutagenesis. Nat Commun. 2015 Jun 16;6:7394. PMID: 26077599.
From the abstract: "... Here, we demonstrate that the A-family polymerase theta (POLQ) is a major driver of inheritable genomic alterations in Caenorhabditis elegans. Unlike somatic cells, which use non-homologous end joining (NHEJ) to repair DNA transposon-induced DSBs, germ cells use polymerase theta-mediated end joining, a conceptually simple repair mechanism requiring only one nucleotide as a template for repair. Also CRISPR/Cas9-induced genomic changes are exclusively generated through polymerase theta-mediated end joining, refuting a previously assumed requirement for NHEJ in their formation. ... "
van Schendel R, Roerink SF, Portegijs V, van den Heuvel S, Tijsterman M. Polymerase Θ is a key driver of genome evolution and of CRISPR/Cas9-mediated mutagenesis. Nat Commun. 2015 Jun 16;6:7394. PMID: 26077599.
From the abstract: "... Here, we demonstrate that the A-family polymerase theta (POLQ) is a major driver of inheritable genomic alterations in Caenorhabditis elegans. Unlike somatic cells, which use non-homologous end joining (NHEJ) to repair DNA transposon-induced DSBs, germ cells use polymerase theta-mediated end joining, a conceptually simple repair mechanism requiring only one nucleotide as a template for repair. Also CRISPR/Cas9-induced genomic changes are exclusively generated through polymerase theta-mediated end joining, refuting a previously assumed requirement for NHEJ in their formation. ... "
Tuesday, June 16, 2015
New online resource for TALE design: SIFTED
The Bulyk lab at Brigham and Women's Hospital has launched the software suite SIFTED, which should be useful to folks designing or interpreting results using Tal Effector Nucleases (TALEs).
Corresponding publication: Rogers JM, Barrera LA, Reyon D, Sander JD, Kellis M, Keith Joung J, Bulyk ML. Context influences on TALE-DNA binding revealed by quantitative profiling. Nat Commun. 2015 Jun 11;6:7440. PMID: 26067805.
Corresponding publication: Rogers JM, Barrera LA, Reyon D, Sander JD, Kellis M, Keith Joung J, Bulyk ML. Context influences on TALE-DNA binding revealed by quantitative profiling. Nat Commun. 2015 Jun 11;6:7440. PMID: 26067805.
Tuesday, June 2, 2015
Actin in the nucleus -- genome-wide cell-based RNAi screen
Excited to see this report on a screen performed by J. Dopie at the DRSC!
Dopie J, Rajakylä EK, Joensuu MS, Huet G, Ferrantelli E, Xie T, Jäälinoja H, Jokitalo E, Vartiainen MK. Genome-wide RNAi screen for nuclear actin reveals a network of cofilin regulators. J Cell Sci. 2015 May 28. pii: jcs.169441. PMID: 26021350.
From the abstract: "Nuclear actin plays an important role in many processes that regulate gene expression. ... Here we have performed a genome-wide RNAi screen in Drosophila cells to identify proteins that influence either nuclear polymerization or import of actin. We validate 19 factors as specific hits, and show that Chinmo/Bach2, SNF4Aγ/Prkag1 and Rab18 play a role in nuclear localization of actin in both fly and mammalian cells. We identify several novel regulators of cofilin activity, and characterize modulators of both cofilin kinases and phosphatase. ... Our screen therefore reveals novel aspects of actin regulation and links nuclear actin to many cellular processes."
Dopie J, Rajakylä EK, Joensuu MS, Huet G, Ferrantelli E, Xie T, Jäälinoja H, Jokitalo E, Vartiainen MK. Genome-wide RNAi screen for nuclear actin reveals a network of cofilin regulators. J Cell Sci. 2015 May 28. pii: jcs.169441. PMID: 26021350.
From the abstract: "Nuclear actin plays an important role in many processes that regulate gene expression. ... Here we have performed a genome-wide RNAi screen in Drosophila cells to identify proteins that influence either nuclear polymerization or import of actin. We validate 19 factors as specific hits, and show that Chinmo/Bach2, SNF4Aγ/Prkag1 and Rab18 play a role in nuclear localization of actin in both fly and mammalian cells. We identify several novel regulators of cofilin activity, and characterize modulators of both cofilin kinases and phosphatase. ... Our screen therefore reveals novel aspects of actin regulation and links nuclear actin to many cellular processes."
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