Special NIH Funding Opportunity: RFA-GM-14-003

The DRSC is specifically mentioned in NIH NIGMS Request for Applications RFA-GM-14-003

"This initiative will provide support for biologists to collaborate with and/or access services of technology resource laboratories, including R01-funded technology developers and specialized centers and resources. Examples of the latter include, but are not limited to ... and the Drosophila RNAi Screening Center. One feature of this initiative is that the biologist, rather than the technology provider, chooses the topic, applies for the funding, and is responsible for the direction of the work."

Funding Opportunity Purpose Statement:

"The purpose of this Funding Opportunity Announcement (FOA) is to diversify and extend the scope and capabilities of currently funded NIGMS R01 and R37 projects for studies on macromolecular interactions and their relationship to function in cells. This FOA solicits revisions (formerly called "competing supplements") of currently funded NIGMS grants specializing in the analysis of molecular systems and mechanisms in live organelles, cells, tissues, or organisms. Applicants may increase their budgets to extend the scientific scope of their projects or to add new approaches that enhance their capabilities for research on macromolecular interactions in cells. Collaboration is not a requirement of this initiative, but applicants may request support for collaboration (including subcontracts) with investigators who have complementary expertise Support for access of modestly funded laboratories to experimental approaches and research objectives that are otherwise financially out of reach is one priority of this FOA."

Application Due-Dates: February 19, 2013 and September 19, 2013.

Click here to view the RFA.

iMAD approach to host-pathogen screening. Breaking report.

These authors report a strategy for simultaneous genetic manipulation of both host (Drosophila cells) and pathogen genes.

O'Connor TJ, Boyd D, Dorer MS, Isberg RR. Aggravating genetic interactions allow a solution to redundancy in a bacterial pathogen. Science. 2012 Dec 14;338(6113):1440-4. doi: 10.1126/science.1229556. PubMed PMID: 23239729.

Systems view of nociception. Breaking report.

This report follows up on a large-scale in vivo RNAi screen. See previous blog post.

Neely GG, Rao S, Costigan M, Mair N, Racz I, Milinkeviciute G, Meixner A, Nayanala S, Griffin RS, Belfer I, Dai F, Smith S, Diatchenko L, Marengo S, Haubner BJ, Novatchkova M, Gibson D, Maixner W, Pospisilik JA, Hirsch E, Whishaw IQ, Zimmer A, Gupta V, Sasaki J, Kanaho Y, Sasaki T, Kress M, Woolf CJ, Penninger JM. Construction of a global pain systems network highlights phospholipid signaling as a regulator of heat nociception. PLoS Genet. 2012 Dec;8(12):e1003071. doi: 10.1371/journal.pgen.1003071. PMID: 23236288.

FlyAtlas Update. Breaking report.

On my desk to read today? This freely accessible report describing new features in FlyAtlas, including the new web interface FlyAtlas 2.

Robinson SW, Herzyk P, Dow JA, Leader DP. FlyAtlas: database of gene expression in the tissues of Drosophila melanogaster. Nucleic Acids Res. 2012 Nov 29. PubMed PMID: 23203866.

GenomeRNAi Update. Breaking Report.

On my desk to read today? This open access update on the DKFZ's GenomeRNAi database of mammalian and Drosophila RNAi screen data.

Schmidt EE, Pelz O, Buhlmann S, Kerr G, Horn T, Boutros M. GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update. Nucleic Acids Res. 2012 Nov 27. PubMed PMID: 23193271.

Targeting PDZ domain-containing proteins. Breaking report.

On my desk to read today? This paper describing the results of in vivo RNAi knockdown of most PDZ domain-containing proteins.

Aranjuez G, Kudlaty E, Longworth MS, McDonald JA. On the role of PDZ domain-encoding genes in Drosophila border cell migration. G3 (Bethesda). 2012 Nov;2(11):1379-91. doi: 10.1534/g3.112.004093. Epub 2012 Nov 1. PubMed PMID: 23173089.

Large-scale RNAi screen. Breaking report.

On my desk to ready today? This disease-relevant report in an open access journal.


Voßfeldt H, Butzlaff M, Prüßing K, Ní Chárthaigh RA, Karsten P, Lankes A, Hamm S, Simons M, Adryan B, Schulz JB, Voigt A. Large-scale screen for modifiers of ataxin-3-derived polyglutamine-induced toxicity in Drosophila. PLoS One. 2012;7(11):e47452. doi: 10.1371/journal.pone.0047452. PubMed PMID: 23139745; PubMed Central PMCID: PMC3489908.

shRNA design. Breaking report.

Gu S, Jin L, Zhang Y, Huang Y, Zhang F, Valdmanis PN, Kay MA. The Loop Position of shRNAs and Pre-miRNAs Is Critical for the Accuracy of Dicer Processing In Vivo. Cell. 2012 Nov 9;151(4):900-11. doi:10.1016/j.cell.2012.09.042. PubMed PMID: 23141545.

Endogenous targets of RNAi. Breaking report.

Bronkhorst AW, van Cleef KW, Vodovar N, Ince IA, Blanc H, Vlak JM, Saleh MC, van Rij RP. The DNA virus Invertebrate iridescent virus 6 is a target of the Drosophila RNAi machinery. Proc Natl Acad Sci U S A. 2012 Nov 14. PubMed PMID: 23151511.

Fly RNAi and Legionella. Recent book chapter.

De Jesús DA, O'Connor TJ, Isberg RR. Analysis of Legionella Infection Using RNAi in Drosophila Cells. Methods Mol Biol. 2013;954:251-64. doi: 10.1007/978-1-62703-161-5_15. PubMed PMID: 23150401.

Endogenous RNAi Functions. Breaking Report.

Yamanaka S, Mehta S, Reyes-Turcu FE, Zhuang F, Fuchs RT, Rong Y, Robb GB, Grewal SI. RNAi triggered by specialized machinery silences developmental genes and retrotransposons. Nature. 2012 Nov 14. doi: 10.1038/nature11716. PubMed PMID: 23151475.

Maternal-Gal4 shRNA system. Breaking report.

Staller MV, Yan D, Randklev S, Bragdon MD, Wunderlich ZB, Tao R, Perkins LA, Depace AH, Perrimon N. Depleting Gene Activities in Early Drosophila Embryos with the "maternal-Gal4 - shRNA" System. Genetics. 2012 Oct 26. PubMed PMID: 23105012.

Touch me! Breaking report.

On my desk to ready today? This paper describing an in vivo RNAi screen of ion channels with larval responses to touch as the output.

Tsubouchi A, Caldwell JC, Tracey WD. Dendritic Filopodia, Ripped Pocket, NOMPC, and NMDARs Contribute to the Sense of Touch in Drosophila Larvae. Curr Biol. 2012 Oct 23. doi:pii: S0960-9822(12)01083-4. 10.1016/j.cub.2012.09.019. PubMed PMID: 23103192.

Breaking Report: Cell Culture

Also on my desk today:

Simcox A. Progress towards Drosophila epithelial cell culture. Methods Mol Biol. 2013;945:1-11. doi: 10.1007/978-1-62703-125-7_1. PMID: 23097097.

Breaking Report: Integrator Complex

On my desk to read today?

Chen J, Ezzeddine N, Waltenspiel B, Albrecht TR, Warren WD, Marzluff WF, Wagner EJ. An RNAi screen identifies additional members of the Drosophila Integrator complex and a requirement for cyclin C/Cdk8 in snRNA 3'-end formation. RNA. 2012 Oct 24. PMID: 23097424.

Breaking Report: in vivo RNAi Screen Focused on Chromosome Instability

On my desk to read today? This open access report on an in vivo RNAi screen.

Shaukat Z, Wong HW, Nicolson S, Saint RB, Gregory SL. A screen for selective killing of cells with chromosomal instability induced by a spindle checkpoint defect. PLoS One. 2012;7(10):e47447. doi: 10.1371/journal.pone.0047447. PMID: 23077619.

Full-Genome Screen Identifies Swell-Activated Chloride Channel. Breaking Report.

On my desk to read today? This open access report of a screen performed at the DRSC.

Stotz & Clapham. Anion-sensitive fluorophore identifies the Drosophila swell-activated chloride channel in a genome-wide RNA interference screen. PLoSOne. 2012;7(10):e46865. doi:10.1371/journal.pone.0046865. PubMed PMID: 23056495.

miRNA Resource. Breaking report.

There are functional and practical at-the-bench connections between RNAi as a technique and the biology of miRNAs. So I try to keep aware of what's happening in the miRNA world, particularly when it comes to new tools. The DRSC makes some miRNA reagents available (e.g. UAS-miRNAs) and miRNA resource collections have been published by various groups. This report describes a new set of tools for interrogating miRNA function.

Schertel1 et al. (2012) in Genetics. Functional Characterization of Drosophila microRNAs by a Novel in vivo Library.  The PubMed citation was not available at the time of this posting. This link should take you to the relevant page at Genetics.

Caution! For in vivo RNAi ageing studies. Recent report.

On my desk to read today? This open access paper reporting effects of in vivo Drosophila RNAi that can confound studies on aging.

Alic N, Hoddinott MP, Foley A, Slack C, Piper MD, Partridge L. Detrimental Effects of RNAi: A Cautionary Note on Its Use in Drosophila Ageing Studies. PLoS One. 2012;7(9):e45367. doi: 10.1371/journal.pone.0045367. PubMed PMID: 23028964.

Then & Now: Jak/Stat screening. Breaking report.

Fisher KH, Wright VM, Taylor A, Zeidler MP, Brown S. Advances in genome-wide RNAi cellular screens: a case study using the Drosophila JAK/STAT pathway. BMC Genomics. 2012 Sep 24;13(1):506. PubMed PMID: 23006893.

Genome RNAi group releases a version 9.0

Esther Schmidt and the GenomeRNAi team just announced a version 9 of their GenomeRNAi online database. Here's a link to their news item on the release.

DIOPT-DIST updated for 'fuzzy' search

The "disease full text search" field at the DRSC's only tool DIOPT-DIST, which is useful for matching up fly (or other model system) genes to human genes associated with diseases or traits, is now more forgiving of misspellings. Trying different synonyms for a given disease is still a good idea. Another tip:  On the search results page, click the DIOPT score to get a protein alignment.

Breaking Report: Cell-basd RNAi protocol

Ravi D, Bishop AJ. Identification of Genes Required for Damage Survival Using a Cell-Based RNAi Screen Against the Drosophila Genome. Methods Mol Biol. 2012;920:9-26. PubMed PMID: 22941593.

Appeal for support letters -- FlyAtlas

The authors of FlyAtlas are appealing for email letters of support as they apply for a new round of funding. If you're a FlyAtlas user, please consider voicing your support. At the DRSC and TRiP, we have seen the resource useful to researchers at both planning and analysis stages. As of this posting, the appeal for email letters of support is on their home page.

Fly App

Not directly RNAi related but I can't resist posting this.

Kumar S, Boccia K, McCutchan M, Ye J. Exploring spatial patterns of gene expression from Fruit Fly embryogenesis on the iPhone. Bioinformatics. 2012 Aug 24. PubMed PMID: 22923306

Novel Assay: Detecting JH

This paper describes an improved approach to detecting farnesoic acid and juvenile hormone. A starting point for a large-scale in vivo RNAi screen perhaps? Open access paper.

Rivera-Perez C, Nouzova M, Noriega FG. A quantitative assay for the juvenile hormones and their precursors using fluorescent tags. PLoS One. 2012;7(8):e43784. PubMed PMID: 22928033

Breaking Report: dsRNA Uptake

Also on my desk to read today?  This paper, which includes a description of what happens following introduction of C. elegans SID-2 into Drosophila S2 cells.

McEwan DL, Weisman AS, Hunter CP. Uptake of Extracellular Double-Stranded RNA by SID-2. Mol Cell. 2012 Aug 14. PMID: 22902558

Breaking Report: F-Box Protein in vivo RNAi Study

On my desk to read today? An in vivo study in which the researchers systematically tested the effects of knockdown of genes encoding F-box-containing proteins.

Dui W, Lu W, Ma J, Jiao R. A Systematic Phenotypic Screen of F-box Genes Through a Tissue-specific RNAi-based Approach in Drosophila. J Genet Genomics. 2012 Aug 20;39(8):397-413. PMID: 22884096.

Breaking Report: Plasmid Toolset for in vivo Expression or RNAi

On my desk to read today? A report of a set of plasmid vectors useful for in vivo expression of various forms of tagged or untagged genes or RNAi constructs.

Wang JW, Beck ES, McCabe BD. A modular toolset for recombination transgenesis and neurogenetic analysis of Drosophila. PLoS One. 2012;7(7):e42102. Epub 2012 Jul 25. PubMed PMID: 22848718

The authors indicate that the plasmids are available at AddGene.

Related resource: pVALIUM and pWALIUM vectors from the Trangenic RNAi Project (TRiP) at Harvard Med School.

Mammalian RNAi Review

On my desk to ready today? A thought-provoking review on progress made and the future of RNAi as a tool in mammalian cells.

Kaelin WG Jr. Molecular biology. Use and abuse of RNAi to study mammalian gene function. Science. 2012 Jul 27;337(6093):421-2. PubMed PMID: 22837515.

Among the recommendations made for the future of mammalian RNAi is screening of smaller focused gene sets with more unique reagents per gene. The DRSC facilitates a similar approach in Drosophila cell-based RNAi screening via availability of deeper-coverage focused or 'sub' libraries and custom dsRNA synthesis for a set of genes based on our existing collection of templates.

Blogmania?

A new blog.


Drosophila Models of Human Disease
www.flydiseasemodels.blogspot.com
The fly community has a general interest in spreading the word about the utility of Drosophila to study human disease. As more gets posted and more experts contribute, we should build a valuable resource with links to papers, fly stocks, relevant tools, and more. If you are interested to contribute a disease summary, highlight a new resource, etc. on a on-time or continuing basis, please get in touch.

Summing it all up so far (created with Wordle)

World's Tiniest Fly

This has nothing to do with RNAi. Or D. melanogaster. But I cannot resist pointing out a recent New York Times article on the world's tiniest fly.

Somatic Homolog Pairing--Genome-Wide Screen

On my desk to read today?  A new report of a screen performed at the DRSC and focused on somatic homolog pairing.  For a related study, check out the Joyce et al. paper mentioned in a previous post.

Bateman et al. (2012) "A Genome-Wide Screen Identifies Genes That Affect Somatic Homolog Pairing in Drosophila" in G3 (Genes, Genomes and Genetics).

On Orthologs, GWAS and Fly Models of Disease

A nice mention of the DRSC Integrative Ortholog Prediction Tool (DIOPT) (Hu et al. in BMC Bioinformatics) appeared recently in a Current Biology dispatch highlighting a Drosophila study investigating genes related to Restless Leg Syndrome.

Shaw & Duntley "Neurological Disorders: Towards a Mechanistic Understanding of Restless Leg Syndrome" Current Biology 22(12).

The study highlighted in the dispatch (Freeman et al. "Sleep fragmentation and motor restlessness in a Drosophila model of restless leg syndrome" Current Biology 22:1142-1148") takes human genome-wide association study (GWAS) data into a model system for functional characterization.

Shaw & Duntley state that "one of the most compelling aspects of the approach of Freeman et al. is the successful use of a model system to functionally characterize a susceptibility gene that was original identified in human genome-wide association studies" and that "the use of model systems to functionally characterize genes identified with genome-wide association studies is a move in the right direction."

At the DRSC, we are excited to see that our bioinformatics tools, as well as our RNAi reagents for cells and in vivo, can have a positive impact on the use of Drosophila to study human disease-related genes and develop disease models.

GenomeRNAi v.8 released

The folks at the DKFZ announced the v.8 release of GenomeRNAi recently. They're up to 127 human RNAi screen data sets and 164 fly RNAi screen data sets.  The fly data sets include screens done at the DRSC, a number of in vivo RNAi screens, and more. Check it out!

Breaking Report: Data Integration Tool

On my desk to read today? A paper describing a data integration tool that might be useful for analysis of RNAi screen data sets.

Renaud et al. (2012) DroPNet: a web portal for integrated analysis of Drosophila protein-protein interaction networks. Nucleic Acids Res. PubMed ID: 22641854

Breaking Report: FISH-based genome-wide screen

On my desk to read today? A new report of a screen done at the DRSC, including use of our confocal screening microscope, and using a novel fluorescence in situ hybridization (FISH)-based approach.

Joyce et al. (2012) Identification of Genes That Promote or Antagonize Somatic Homolog Pairing Using a High-Throughput FISH-Based Screen.  PLoS Genet. PubMed ID: 22589731.

Testing 1, 2, 3

Recently we have received a number of questions along the lines of, "How much dsRNA should I use and how many cells?"

If you are doing a screen with our libraries, we offer two different concentrations of dsRNA (one recommend for the bathing method, the other recommend for transfection). As a result, you can change cell number but you're stuck with our dsRNA concentrations. Thus, you should optimize things with those concentrations in mind, and for 384-well format plates.

If, however, you are designing a smaller-scale study or otherwise have control over dsRNA concentrations, you can play around with both dsRNA and cell concentrations, in various plate formats, in order to find an optimal set-up for your assay. Above is an example layout for testing what concentration of dsRNA and cells to use for an assay. In this case, we were designing a test for a 96-well format experiment using the bathing method of dsRNA delivery. We chose dsRNA directed against thread (th) as a positive control for RNAi and did a read-out of cell viability to assess knockdown. Including several negative controls (LacZ and EGFP in addition to empty wells) allowed us to make sure dsRNAs did not reach non-specific toxic levels and get a sense of the overall variability of the assay. In our test, wells in columns 1 and 2 got the smallest number of cells and less dsRNA, and wells in columns 11 and 12 got the largest number of cells and more dsRNA.

For other plate formats, other dsRNA delivery methods, different cell types, etc. you can use the same general strategy to design a test and carefully determine an optimal set of conditions for your assay. Doing this type of testing at the beginning can save time and improve results later in the process.

Breaking Report: Looking at long non-coding RNAs

On my desk to ready today? Report of an approach based on RNAi and RNA FISH that is useful for the study of long non-coding RNAs (lncRNAs).

Chakraborty (2012) Combined RNAi and localization for functionally dissecting long noncoding RNAs. Nature Methods 9:360–362.

GenomeRNAi Announces v7.0

The folks at GenomeRNAi just announced release of a version 7.0 of their database, including 28 newly available human cell-based RNAi screen data sets.

Breaking Report: Regulators of Hh Secretion

On my desk to read today? A report on a full-genome screen performed at the DRSC.

The authors include information that might be generally useful to screeners, particularly those performing or currently analyzing the results of luciferase-based assay readouts. The study also includes follow-up using in vivo RNAi.

Aikin et al. (2012) A Genome-Wide RNAi Screen Identifies Regulators of Cholesterol-Modified Hedgehog Secretion in Drosophila. PLoS One. 2012;7(3):e33665. PubMed ID: 22432040

FlyMine v33.0

FlyMine recently announced a version 33.0. Details on changes on their blog.

Breaking Report: Proteasome Components & Apical Localization

Also on my desk to read today? A report that includes an in vivo RNAi screen and another that includes screening with deficiencies, classical alleles and in vivo RNAi.

Yano et al. (2012) Identification of proteasome components required for apical localization of Chaoptin using functional genomics. J. Neurogenet. Mar 14. PubMed ID: 22417167

Tan et al. (2012) Genetic screen for regulators of lymph gland homeostasis and hemocyte maturation in Drosophila. G3. 2(3):393-405. PubMed ID: 22413093

Upcoming: Special Issue on RNAi in Genes

The journal Genes is planning a special open access issue on RNA interference.

Website: http://www.mdpi.com/si/genes/RNA_interference/
Guest Editor: Prof. Dr. Jeremy C. Simpson
Deadline for manuscript submissions: 15 August 2012

The Structure of Human Dicer

On my desk to read today? A paper that provides insight into Dicer function.

Lau PW, Guiley KZ, De N, Potter CS, Carragher B, Macrae IJ. The molecular architecture of human Dicer. Nat Struct Mol Biol. 2012 Mar 18. PubMed ID: 22426548

FlyBase Survey

Fly people: Take the FlyBase survey! This is our opportunity to be counted as active FlyBase users and make suggestions they will follow up on in future years!

Breaking Report: Cross-system look at the Beta Catenin destruction complex

On my desk to read today? A study that combines cell-based RNAi and in vivo studies in Drosophila with studies in human cultured cells to look at the beta-Catenin destruction complex.

Roberts et al. (2012) Defining components of the bcatenin destruction complex and exploring its regulation and mechanism of action during development. Open Access in PLoS One.

Local? Assay Technology Seminar

If you are local to HMS you might want to check out the assay technology series seminar hosted by the ICCB-Longwood on Wed. Feb. 1. Details online.

New version of Genome RNAi

The Boutros group has launched a version 6 of GenomeRNAi. According to their announcement, the database now contains data from about 100 human cell-based RNAi screens, about 100 fly cell-based RNAi screens (including DRSC screen data), and about 50 in vivo fly RNAi screens. They also now offer the option to input your own data. Check it out!

Breaking Report: Moesin Dephosphorylation

On my desk to read today? A report of an RNAi screen focused on phosphatases.

Kunda et al. 2012 PP1-Mediated Moesin Dephosphorylation Couples Polar Relaxation to Mitotic Exit. Curr Biol. ePubed 2011 Dec 28. PubMed ID: 22209527

DIOPT & DIOPT-DIST Updated

We recently updated the underlying data sets in DIOPT and DIOPT-DIST. There will be some new relationships (for example, new human gene-fly gene relationships). So if you've searched before it's worth repeating the search. For details feel free to contact the DRSC bioinformatics staff.