Arthropod Genomics 2014

Passing along an announcement for Arthropod Genomics 2014. The deadline to submit abstracts is April 17, 2014, and the deadline for early registration is April 21, 2014.

Luciferase-based assays in cultured cells

Yun C, Dasgupta R. Luciferase reporter assay in Drosophila and Mammalian tissue culture cells. Curr Protoc Chem Biol. 2014 Mar 14;6(1):7-23. PMID: 24652620.

Not RNAi -- Methods chapter on other ways to interrogate gene function in flies

Venken KJ, Bellen HJ. Chemical mutagens, transposons, and transgenes to interrogate gene function in Drosophila melanogaster. Methods. 2014 Feb 28. pii: S1046-2023(14)00069-3. PMID: 24583113.

Single-cell analysis of S2R+ RNAi screen image data

Dey G, Gupta GD, Ramalingam B, Sathe M, Mayor S, Thattai M. Exploiting cell-to-cell variability to detect cellular perturbations. PLoS One. 2014 Mar 4;9(3):e90540. PMID: 24594940; PMCID: PMC3942435.

DRSC & TRiP at ADRC

Are you at the ADRC? So are we. Posters 855C and 857B.

New CRISPR tools at DRSC--Find CRISPR2 and Efficiency Tool

Interested in CRISPRs in flies? Check out the new version of our Find CRISPRs tool, Find CRISPRs Version 2, and new Efficiency Predictor that assigns a score to a given short guide RNA sequence.

The DRSC offers CRISPR design help, CRISPR sgRNA construct production and donor construct production. You can view services and our low prices, as well as place requests, at the website of the new Genome Engineering Production Group at the DRSC at HMS. We can send custom-made constructs to you or directly to a commercial Drosophila injection company.

CRISPR in flies with novel non-coding gene promoter driving expression of the short guide RNA

New report in G3: Xue, Ren, Wu, Dai, Rong and Gao. Efficient Gene Knock-Out and Knock-In with Transgenic Cas9 in Drosophila. Early online access.

Use of fly cells to study the cytoskeleton

Nye J, Buster DW, Rogers GC. The use of cultured Drosophila cells for studying the microtubule cytoskeleton. Methods Mol Biol. 2014;1136:81-101. PMID: 24633795.

From the abstract:  The authors "describe basic techniques for gene knockdown, transgene expression, preparation for fluorescence microscopy, and centrosome enrichment using cultured Drosophila cells with an emphasis on studying the microtubule cytoskeleton."

Full-genome RNAi screen in S2 cells looks at RAS/MAPK signaling

Ashton-Beaucage D, Udell CM, Gendron P, Sahmi M, Lefrançois M, Baril C, Guenier AS, Duchaine J, Lamarre D, Lemieux S, Therrien M. A Functional Screen Reveals an Extensive Layer of Transcriptional and Splicing Control Underlying RAS/MAPK Signaling in Drosophila. PLoS Biol. 2014 Mar 18;12(3):e1001809. PMID: 24643257.

Use of tissue-specific RNAi to help assess "biological quality" in RNA-seq data

Amaral AJ, Brito FF, Chobanyan T, Yoshikawa S, Yokokura T, Van Vactor D, Gama-Carvalho M. Quality assessment and control of tissue specific RNA-seq libraries of Drosophila transgenic RNAi models. Front Genet. 2014 Mar 5;5:43. PMID: 24634674.

Life in a bubble

At the DRSC we recently tested a new commercial plate type supporting growth of cells in very small volumes of media--tiny domes of liquid in 96- or 384-well format. We have not had time for much testing but we can say this:  S2R+ cultured Drosophila cells grew just fine in this format in our hands. Photo below. Feel free to email the DRSC Director if you have any questions. DropArray plates from Curiox. Posting this for information purposes only (should not be considered an endorsement).

Large-scale in vivo RNAi screen for factors related to germline stem cells

Yan D, Neumüller RA, Buckner M, Ayers K, Li H, Hu Y, Yang-Zhou D, Pan L, Wang X, Kelley C, Vinayagam A, Binari R, Randklev S, Perkins LA, Xie T, Cooley L, Perrimon N. A regulatory network of Drosophila germline stem cell self-renewal. Dev Cell. 2014 Feb 24;28(4):459-73. PMID: 24576427.

From the abstract: "... To comprehensively identify components of these networks, we performed a large-scale RNAi screen in Drosophila female germline stem cells (GSCs) covering ∼25% of the genome. The screen identified 366 genes that affect GSC maintenance, differentiation, or other processes involved in oogenesis. Comparison of GSC regulators with neural stem cell self-renewal factors identifies common and cell-type-specific self-renewal genes. ..."

These authors deposited screen data into RSVP, the TRiP's RNAi Stock Validation and Phenotypes data repository. Additional data submissions welcome!  Check it out online here.

Methods paper on fly RNAi in cells and in vivo

Humbly offered by your blog author ...


Mohr SE. RNAi screening in Drosophila cells and in vivo. Methods. 2014 Feb 24. pii: S1046-2023(14)00062-0. PMID: 24576618.

Interplay of RNAi, cell death and tranposons

Birchler JA. Does ectopic cell death cause somatic mutations in the neighboring cells by activating transposons? Mob Genet Elements. 2014 Jan 1;4(1):e28040. PMID: 24567848.

Genome-wide RNAi screen for host factors related to West Nile Virus

Yasunaga A, Hanna SL, Li J, Cho H, Rose PP, Spiridigliozzi A, Gold B, Diamond MS, Cherry S. Genome-Wide RNAi Screen Identifies Broadly-Acting Host Factors That Inhibit Arbovirus Infection. PLoS Pathog. 2014 Feb 13;10(2):e1003914. PMID: 24550726; PMCID: PMC3923753.

From the abstract:  "Investigation of two newly identified factors that restrict diverse viruses, dXPO1 and dRUVBL1, in the Tip60 complex, demonstrated they contributed to antiviral defense at the organismal level in adult flies, in mosquito cells, and in mammalian cells. These data suggest the existence of broadly acting and functionally conserved antiviral genes and pathways that restrict virus infections in evolutionarily divergent hosts."