FlyRNAi

Local? Assay Technology Seminar

2012-01-30T16:32:00.003-05:00

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

2012-01-13T14:53:00.004-05:00

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

2012-01-10T14:57:00.002-05:00

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

2012-01-05T10:44:00.003-05:00

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.

Annual Arthropod Meeting Announcement

2011-12-14T16:09:00.003-05:00

I recently saw an announcement for the Sixth Annual Arthropod Genomics Symposium. May 31, 2012 to June 2, 2012 in Kansas City (i5K workshop May 30-31). Details on their website.

NIH Funding Opportunities

2011-12-14T13:19:00.004-05:00

The NIH has announced new funding opportunities for small molecule screening at established academic screening centers like the DRSC.

From the FAO purpose statement: "This Funding Opportunity Announcement (FOA) encourages investigators to form collaborations with an established academic, nonprofit, or commercial high throughput screening (HTS) facility that has the requisite expertise and experience to implement HTS-ready assays for the discovery and development of small molecule chemical probes."

Check out these announcements at NIH for more information and please feel free to get in touch if you'd like to collaborate on a small molecule screening project.

PAR-12-058 Solicitation of Assays for High Throughput Screening (HTS) to Discover Chemical Probes (R01)
PAR-12-059 Solicitation of Assays for High Throughput Screening (HTS) to Discover Chemical Probes (R21)
PAR-12-060 Solicitation of Validated Hits for the Discovery of in vivo Chemical Probes (R01)

Breaking Report: Public Engagement in Fly Research

2011-12-06T15:42:00.002-05:00

On my desk to read today? A bit of a departure from RNAi. This paper on engaging the public in Drosophila research caught my eye.

Pulver et al. (2011) Why flies? Inexpensive public engagement exercises to explain the value of basic biomedical research on Drosophila melanogaster. Adv Physiol Educ. 35(4):384-92. PubMed ID: 22139775.

DRSC Database Note

2011-12-01T09:04:00.004-05:00

The DRSC database was recently updated to FlyBase release 41 (had been 39).

Breaking Report: Cross-Species Transgenesis

2011-11-17T09:18:00.006-05:00

Also on my desk today--a pair of papers on techniques relevant to cross-species RNAi rescue.

Ejsmont et al. (2011) Recombination-mediated genetic engineering of large genomic DNA transgenes. Methods Mol Biol. 772:445-58. PubMed ID: 22065454.

Ejsmont et al. (2011) Production of fosmid genomic libraries optimized for liquid culture recombineering and cross-species transgenesis. Methods Mol Biol. 772:423-43. PubMed ID: 22065453.

Breaking Report: Ecdysone Receptor Co-Factors

2011-11-17T09:06:00.002-05:00

Also on my desk today? Catching up on a new small-scale fly cell RNAi screen. The authors tested one dsRNA per gene with several different cell lines in this focused study.

Davis et al. (2011) Identification of common and cell type specific LXXLL motif EcR cofactors using a bioinformatics refined candidate RNAi screen in Drosophila melanogaster cell lines. BMC Dev Biol. 11(1):66. PubMed ID: 22050674.

Reminder: The DRSC can help with small-scale screens by building custom libraries in 96- or 384-well plates based on our existing libraries of templates.

Breaking Report: Stable Cell Lines

2011-11-17T09:04:00.004-05:00

On my desk today? A new report on making stable cell lines.

Gonzalez et al. (2011) Generation of stable Drosophila cell lines using multicistronic vectors. In Nature's Scientific Reports. DOI: 10.1038/srep00075

DRSC Database Paper

2011-11-16T15:55:00.004-05:00

Our database update paper is published. As always, feedback on the database and website is welcome. I'm hoping to catch up with some breaking research reports soon.

Flockhart et al. (2011) FlyRNAi.org--the database of the Drosophila RNAi screening center: 2012 update. Nucleic Acids Res. PubMed ID: 22067456.

Breaking Report: The ERK Signal Transduction Pathway

2011-10-28T13:28:00.005-04:00

On my desk today? A paper that includes data from two screens performed at the DRSC. The screen datasets are available on our website--one way to access them is via the Experimental Data links following the listing for the paper on this page.

Friedman et al. (2011) Proteomic and functional genomic landscape of receptor tyrosine kinase and ras to extracellular signal-regulated kinase signaling. Sci Signal. 4(196):rs10. PubMed: 22028469.

Breaking Report: Rab5 & Chromosome Alignment

2011-10-18T10:30:00.004-04:00

On my desk to ready today? A report on Rab5 GTPase and chromosome alignment. I confess that what drew me to the paper is technique, as the report includes live-cell imaging following RNAi, as well as simultaneous knockdown of two genes via RNAi.

Capalbo et al. (2011) Rab5 GTPase controls chromosome alignment through Lamin disassembly and relocation of the NuMA-like protein Mud to the poles during mitosis. Proc Natl Acad Sci U S A. PMID: 21987826.

Breaking Report: Review of Host-Pathogen Interaction Interactions

2011-10-14T10:39:00.006-04:00

On my desk to read today? A review of work in the field of host-pathogen interactions. Studies at the DRSC and elsewhere using Drosophila cell-based RNAi have had an impact in the field.

Bier and Guichard (2011) Deconstructing host-pathogen interactions in Drosophila.
Dis Model Mech. PMID: 21979942.

Plate-to-List, List-to-Plate Conversion Tool

2011-10-11T16:59:00.005-04:00

If you have ever copy-and-pasted data displayed like a 96- or 384-well plate to convert it to a simple list, or vice versa, then I expect you'll appreciate our newest online tool, the Plate-to-List, List-to-Plate conversion tool. It's designed for use with spreadsheets. We're finding it handy for some of our in-house stuff and expect it will be convenient for others as well. Big thanks to Ian Flockhart for developing the tool and getting it launched on the web very quickly!

DIOPT-DIST Updated

2011-10-06T14:44:00.003-04:00

Our DIOPT-DIST tool was recently updated. Data from about 200 new GWAS studies was added. More info about the tool in the DIOPT paper and please feel free to ask us if you have questions.

Breaking Report: Shedding Light on NFkB

2011-10-05T08:53:00.002-04:00

And yet another breaking paper on my desk today ...

Valanne et al. (2011) Large-scale RNAi screens add both clarity and complexity to Drosophila NFkB signaling. Dev Comp Immunol. PubMed ID: 21930155

Breaking Report: Neddylation & Hedgehog

2011-10-05T08:49:00.004-04:00

Another breaking report on my desk to read today:

Du et al. (2011) In vivo RNAi scren reveals neddylation genes as novel regulators of hedgehog signaling. PLoS One. 6(9):e24168. PubMed ID: 21931660

Breaking Report: Review of RNAi screening

2011-10-05T08:42:00.003-04:00

Norbert and I have a new review out that discusses cell-based and in vivo RNAi in various species and emphasizes interaction of the RNAi screening field with other fields of study.

Mohr & Perrimon (2011) RNAi screening: new approaches, understandings, and organisms. Wiley Interdiscip Rev RNA. doi: 10.1002/wrna. PubMed ID: 21953743

Breaking Report: The D17-c3 Cell Culture System

2011-10-05T08:37:00.003-04:00

This paper describes use of D17-c3 cells. As the authors point out, a relatively small number of cell types are typical for RNAi screens but a large number of others are available from the DGRC.

Currie & Rogers (2011) Using the Drosophila melanogaster D17-c3 cell culture system to study cell motility. Nat Protoc 6(10):1632-41. PubMed ID: 21959242

Breaking Report: Review--Fly as Disease Model

2011-10-05T08:34:00.004-04:00

I think this review on using Drosophila as a model to study cardiac function has a very nice introduction to molecular genetic methods--good reading for someone new to fly research.

Wolf & Rockman (2011) Drosophila, genetic screens, and cardiac function. Circ Res 109(7):794-806. PubMed ID: 21921272

Catching up

2011-10-05T08:31:00.003-04:00

I'm back in town after a couple of weeks off. Prepare for a flurry of posts on breaking reports! And as always, if I've missed something, please feel free to email or comment to let me know.

Meeting Announcement--Crete

2011-09-09T10:43:00.003-04:00

I recently received an announcement for the EMBO Conference in Crete, The Molecular and Developmental Biology of Drosophila. Registration closes Nov. 1, 2011 for this June 2012 meeting.

Breaking Report: Full-Genome Screen for Wg Secretion Regulators

2011-09-05T09:51:00.004-04:00

On my desk to read today?

A report on a full-genome cell-based RNAi screen performed here at the DRSC.

Port et al. (2011) A genome-wide RNA interference screen uncovers two p24 proteins as regulators of Wingless secretion. EMBO Rep. doi: 10.1038/embor.2011.165. PMID: 21886182.

Breaking Report: Huntington's Disease Model Study

2011-09-05T09:30:00.006-04:00

On my desk today? A very recent report from Schulte, Sepp et al. using Drosophila primary cells. The study included screening of the DRSC Kinases & Phosphatases library.

Schulte, et al. (2011) High-Content Chemical and RNAi Screens for Suppressors of Neurotoxicity in a Huntington's Disease Model. Open access at PLoS One 6(8): e23841

DRSC's DIOPT and DIOPT-DIST

2011-08-31T09:18:00.005-04:00

Sneak peak for blog readers: Our new ortholog-related tools DIOPT and DIOPT-DIST are available online and a provisional version of the paper describing the tools is also available at BMC Bioinformatics. As always, your feedback on our web-based tools is welcome!

Methods Papers

2011-08-29T10:41:00.004-04:00

There are at least two papers in volume 782 of Methods in Molecular Biology that may be relevant to cell-based Drosophila RNAi screening:

Davidson JM, Duronio RJ. (2011) Using Drosophila S2 Cells to Measure S phase-Coupled Protein Destruction via Flow Cytometry. Methods Mol Biol. 782:205-219. PMID: 21870294.

Siudeja K, de Jong J, Sibon OC. (2011) Studying Cell Cycle Checkpoints Using Drosophila Cultured Cells. Methods Mol Biol. 782:59-73. PMID: 21870285.

Breaking Reports

2011-08-23T09:38:00.005-04:00

On my desk to read today? Two reports related to fly RNAi studies from the Boutros group and collaborators, describing a computational approach for use with double-knockdown data and a species-spanning study related to TOR pathway signaing.

Axelsson et al. (2011) Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAi. BMC Bioinformatics. 12(1):342. PMID: 21849035.

Zacharogianni et al. (2011) ERK7 is a negative regulator of protein secretion in response to amino-acid starvation by modulating Sec16 membrane association. EMBO J. doi: 10.1038/emboj.2011.253. PMID: 21847093.

Tech Tips: Minimizing Well Volume Loss

2011-08-17T09:58:00.006-04:00

I recently replied to a question about minimizing variability in the volume of liquid present in a well at the end of a cell-based RNAi experiment. It is important to minimize variability in the volumes well-to-well, as variability can affect the assay and/or the assay readout, causing 'noise' in the screen that obscures meaningful results. Because others might have similar concerns, I'll post a summary of my answers here.

Variability in micro-plate well volumes is usually due to equipment issues or evaporation. We recommend the following steps to limiting problems.

(1) Have your pipetting or automated liquid handling equipment calibrated, and keep it clean and clog-free. If one row or column is consistently different from the others, that can suggest you have a clog or another equipment problem.

(2) Make sure the equipment you are using is accurate in the range of volumes you are using. You would not use a P-1000 hand-held pipettor to measure 2 microliters of volume, as a P-1000 is not considered accurate in that range. Similar to this, automated liquid handling instruments are considered accurate in only within specific ranges, and should be used accordingly.

(3) In addition to using a humidified incubator, we recommend also putting the plates inside plastic containers with damp paper towels at the bottom, to help minimize evaporation loss.

(4) Take all appropriate steps to limit "false discovery" due to any cause, including: establish good positive and negative controls, make sure you have a good signal-to-noise before screening, perform replicate tests when you screen, use appropriate statistical analyses to identify screen hits, and experimentally test initial screen hits with other reagents and assays.

Breaking Reports: Validation, Screening & in vivo Technologies

2011-08-16T10:00:00.008-04:00

On my desk to read today? A couple of new cell-based screen-related papers--one of which systematically tests orthologs of candidate genes culled from fly screens in human cells--and a report on recombinases newly available for use in Drosophila. The report on recombinases is not directly relevant to fly RNAi but I'm including it because what's described should be of general interest to Drosophila researchers--yet another new tool in our ever-growing molecular genetic toolbox.

Bai et al. (2011) Identification and characterization of a set of conserved and new regulators of cytoskeletal organisation, cell morphology and migration. BMC Biol. 9(1):54. PMID: 21834987.

Dubrovsky et al. (2011) The Drosophila FTZ-F1 nuclear receptor mediates juvenile hormone activation of E75A gene expression through an intracellular pathway. J Biol Chem. PMID: 21832074.

Nern et al. (2011) Multiple new site-specific recombinases for use in manipulating animal genomes. Proc Natl Acad Sci U S A. PMID: 21831835.

Breaking Report: Review by FAQs--Common Screening Center Questions Clarified

2011-08-15T10:33:00.006-04:00

On my desk to read today? A review of common questions posed to screening centers--and answers to the questions--from a center in the UK. Recommended reading for potential screeners and for screening center personnel.

Jiang M et al. (2011) Tales from an academic RNAi screening facility; FAQs. Brief Funct Genomics. 10(4):227-37. PMID: 21527443

Breaking Report: a lac operon system for expression in S2 cells

2011-08-11T09:10:00.003-04:00

On my desk to read today? A report describing use of the lac operon system for inducible expression of a transgene in S2 cells.

Wakiyama et al. (2011) Inducible protein expression in Drosophila Schneider 2 cells using the lac operator-repressor system. Biotechnol. Lett. PMID: 21826399.

Batch Search of TRiP Tools

2011-08-04T08:45:00.003-04:00

Sneak peek for blog readers: here's a link to a batch search tool for TRiP stocks. Feedback welcome. It will be linked to from TRiP web pages on in vivo fly RNAi resources soon. Upload files should be .txt with one gene symbol (or other identifier) per line.

The DKFZ's GenomeRNAi turns 5.0

2011-08-04T08:38:00.005-04:00

I just learned that the Boutros group at DKFZ has launched a "5.0" version of their GenomeRNAi database. Results from DRSC screens, other fly and mammalian cell-based screens, and fly in vivo screens are searchable at GenomeRNAi. Check it out!

Publications on GenomeRNAi are listed here.

Cross-Species Validation with Live Imaging--Cell Cycle Screen Hits

2011-08-02T09:44:00.006-04:00

Also on my desk today? A report from Sironi et al. using living mammalian cell imaging and analysis to follow up on hits from RNAi screens related to the cell cycle performed in other species.

Sironi et al. (2011) Automatic quantification of microtubule dynamics enables RNAi-screening of new mitotic spindle regulators. Cytoskeleton 68:266-278.

New Editorial & Report: Phagocytosis of Bacteria

2011-08-02T09:36:00.006-04:00

On my desk this morning? A review by Flannagan and Grinstein on the use of knockdown approaches in Drosophila and zebrafish to study phagocytosis of bacteria. The original article is Ulvila et al. (2011). Info on both below.

Flannagan & Grinsten (2011) Fly fishing with RNAi catches novel effectors of phagocytosis. J. Leukoc. Biol. 89:643-645.

Ulvila et al. (2011) Cofilin regulator 14-3-3[] is an evolutionarily conserved protein required for phagocytosis and microbial resistance. J. Leukoc. Biol. 89:649-659.

Breaking Report: RNAi Pathways

2011-07-26T10:17:00.003-04:00

On my desk to ready this morning? A new report that suggests the possibility of a Dicer-independent pathway for generation of siRNAs in flies.

Tchurikov & Kretova (2011) Both piRNA and siRNA Pathways Are Silencing Transcripts of the Suffix Element in the Drosophila melanogaster Germline and Somatic Cells. PLoS One. 6(7):e21882. PubMed ID: 21779345

Breaking Report: New Review

2011-07-18T10:23:00.003-04:00

On my desk to read this morning? A new review from C. Bakal that includes discussion of complex image-based readouts as well as other topics in fly RNAi screening.

Bakal C. (2011) Drosophila RNAi screening in a postgenomic world. Brief Funct. Genomics. PubMed PMID: 21752787.

Breaking Report: RNAi Pathway & Lysosome-Related Organelles

2011-07-13T10:09:00.002-04:00

On my desk to read this morning? A report related to the endogenous biology of the RNAi pathway.

Harris et al. (2011) Cargo sorting to lysosome-related organelles regulates siRNA-mediated gene silencing. J Cell Biol. 194(1):77-87. PMID: 21746852.

Breaking Report: Role for RNAi Pathway in Chromosome Segregation

2011-07-07T14:55:00.004-04:00

Also on my desk to read today?

Pek & Kai (2011) DEAD-box RNA helicase Belle/DDX3 and the RNA interference pathway promote mitotic chromosome segregation. Proc Natl Acad Sci U S A. PMID: 21730191.

Breaking Report: RNAi & Cell Death

2011-07-07T13:36:00.002-04:00

On my desk today? A report of a possible link between RNAi pathway activity and cell death.

Xie et al. (2011) Inhibition of RNA Interference and Modulation of Transposable Element Expression by Cell Death in Drosophila. Genetics. PMID: 21596898.

Breaking Report: Chemical Screen in RNAi knockdown background

2011-07-05T08:22:00.002-04:00

On my desk to read this morning? A chemical screen in a background sensitized by RNAi. Screened in fly cells with follow-up in a mammalian system.

Gonsalves et al. 2011. An RNAi-based chemical genetic screen identifies three small-molecule inhibitors of the Wnt/wingless signaling pathway. Proc Natl Acad Sci U S A. 108(15):5954-63. PMID: 21393571; PubMed Central PMCID: PMC3076864.

Breaking Report: Pathogen Screen

2011-06-24T10:51:00.008-04:00

On my desk to read today? A pathogen screen in S2 cells.

Qin et al. (2011) Functional Analysis of Host Factors that Mediate the Intracellular Lifestyle of Cryptococcus neoformans. PLoS Pathog. 7(6):e1002078. PMID: 21698225.

Similar interest in screening a relatively small set of genes? The DRSC will cherry-pick from our collection of high-quality amplicons and make dsRNA for your custom screen.

Going for the Kill

2011-06-20T09:17:00.005-04:00

On my desk to read today? A paper that describes using in vivo RNAi to sensitize strains, then test potential insecticides for activity that might otherwise be masked by a wild-type organism's ability to detox.

Shah et al. (2011) Insecticide detoxification indicator strains as tools for enhancing chemical discovery screens. Pest Manag Sci. doi: 10.1002/ps.2218. PMID: 21681918.

Kinases & Phophatases

2011-05-26T09:42:00.004-04:00

The list associated with the DRSC Kinases & Phosphatases library has been updated.

The downloadable spreadsheet now indicates which genes encode known or predicted kinases, and which encode known or predicted phosphatases. The new list also shows the updated FlyBase IDs (FBgn Numbers) and gene symbols, along with the IDs and symbols that appeared on the older version of the list. The library has close to 3 unique reagents per gene.

On the assay plates themselves, the two categories are mixed up together so it's not possible to screen just kinases or just phosphatases (we get asked that fairly often).

Breaking Report: Addressing Off-Target Effects

2011-05-25T10:32:00.003-04:00

On my desk to read today? A new paper looking at off-target effects.

Seinen et al. (2011) RNAi-induced off-target effects in Drosophila melanogaster: frequencies and solutions. Briefings in Functional Genomics. PMID: 21596801.

Just for Fun

2011-05-24T13:01:00.003-04:00

Got lightning fast cells? Enter them in the World Cell Race!

Breaking News: RNAi Uptake

2011-05-12T12:28:00.002-04:00

On my desk to read today? Usually we try hard to keep bacteria out of our cell cultures. But this group used E. coli that express dsRNAs to address possible routes for RNAi uptake.

Rocha et al. (2011) A Phagocytic Route for Uptake of Double-Stranded RNA in RNAi. Open Access at PLoS ONE. PMID: 21559499.

Breaking Report: Stem Cells

2011-05-11T14:28:00.002-04:00

Also on my desk today, a new report on self-renewal.

Neumüller et al. (2011) Genome-Wide Analysis of Self-Renewal in Drosophila Neural Stem Cells by Transgenic RNAi. Cell Stem Cell. 8(5):580-93. PMID: 21549331

Breaking Report: Exploring False Discovery

2011-05-11T14:20:00.001-04:00

On my desk to read today? A study that uses multiple high-throughput data sources to look at false discovery.

Guest et al. (2011) A protein network-guided screen for cell cycle regulators in Drosophila. BMC Systems Biology. 5(1):65. PMID: 21548953

Breaking Report: ER Proteins

2011-05-06T12:12:00.002-04:00

Also on my desk?

Kondylis et al. (2011) Identification of ER proteins involved in the functional organisation of the early secretory pathway in Drosophila cells by a targeted RNAi screen. Open Access at PLoS One.

Breaking Report: Parkinson's Disease Screen

2011-05-06T12:10:00.001-04:00

On my desk today?

Fernandes & Rao (2011) Genome-wide screen for modifiers of Parkinson's disease genes in Drosophila. Mol. Brain. PMID: 21504582

Answers Online!

2011-05-06T11:07:00.001-04:00

The DRSC has just added a FAQs page based on real actual questions we have received over the past few years (and a few made up ones as well, of course!). Feedback welcome!

Breaking Report: Cell Profiler 2.0

2011-04-18T11:18:00.002-04:00

On my desk to read today? A report on an updated version of the open source Cell Profiler software for screen image data analysis.

Kamentsky et al. (2011) Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software. Bioinformatics. 27(8):1179-80.

Breaking Report: RNA Splicing

2011-04-15T09:30:00.004-04:00

I haven't quite got my hands on a copy of the article yet but I am looking forward to reading this:

Ashton-Beaucage and Therrien (2011) The exon junction complex: A splicing factor for long intron containing transcripts? Fly. Jul 1;5(3). PMID: 21478676

Even more catching up to do

2011-04-12T17:05:00.008-04:00

Later the same day, and I'm still catching up on past posts. Here is another I might have missed--UPDATE: No, I didn't. It was posted. But I'll leave this up anyway.

Saj et al. (2010) A combined ex vivo and in vivo RNAi screen for notch regulators in Drosophila reveals an extensive notch interaction network. Dev Cell. 2010 May 18;18(5):862-76.

In the future I might start tagging by topic and/or authors. Make it easier for myself and others to figure out what was posted before.

Breaking Report (Catching up!): 14-3-3zeta in phagocytosis and resistance, and, AP-3 in sorting

2011-04-12T13:09:00.004-04:00

On my desk today? Catching up on two papers I think I missed.

Ulvila et al. (2011) Cofilin regulator 14-3-3{zeta} is an evolutionarily conserved protein required for phagocytosis and microbial resistance. J Leukoc Biol. PMID: 21208897

Asensio et al. (2010) RNAi screen identifies a role for adaptor protein AP-3 in sorting to the regulated secretory pathway. J Cell Biol. 2010 Dec 13;191(6):1173-87.

If you see something appropriate to the blog that I seem to have missed, please feel free to let me know by commenting on the blog or by email!

Web Wednesday: Antibodies against Drosophila Antigens

2011-04-06T11:23:00.002-04:00

Just got notification of new additions in the set of antibodies against Drosophila antigens present in the collection at the Developmental Studies Hybridoma Bank. Take a look.

Breaking Report from the Transgenic RNAi Project (TRiP)

2011-04-05T11:09:00.003-04:00

On my desk today? A breaking report from our lab space colleagues with the Transgenic RNAi Project (TRiP) here at Harvard Med School.

Ni et al. (2011) A genome-scale shRNA resource for transgenic RNAi in Drosophila. Nature Methods (e-published today ahead of print). PMID: 21460824.

Web Wednesday--ADRC Special Edition!

2011-03-30T21:31:00.004-04:00

Today, a Web Wednesday report, coming to you live from the Drosophila conference!

We've just launched our online web tool for ortholog predictions: the DRSC Integrative Ortholog Prediction Tool (DIOPT). Building on work from many other groups, we've created an integrative tool that displays results from many tools. We've also included features meant to make it easier for biologists to search and view ortholog predictions.

Details and more at Poster 452B (Hu et al.).

Please check it out and let us know if you have suggestions for improvement!

Methods Reports

2011-03-28T12:45:00.003-04:00

There are Drosophila RNAi-related reports in a recent Methods in Molecular Biology series book (volume 721). Can't yet say that I'm reading them (don't have copies yet). But they've shown up in PubMed and I did want to make an announcement. Includes reports from S. Cherry, Obadia & Saleh, Nayak & Andino, Yang & Li, and van Cleef et al.

A year of assays for free?

2011-03-24T12:00:00.002-04:00

Looks like a 1,000-word essay could win you free access to an Acumen laser scanning cytometer for a year. Here's hoping a Drosophila researcher gets picked!

Breaking Report: RNAi "sensor arrays" and RNAi design

2011-03-18T11:52:00.002-04:00

On my desk to read today? A newly reported approach to identification of potent shRNAs.

Fellmann et al. 2011 Functional Identification of Optimized RNAi Triggers Using a Massively Parallel Sensor Assay. Molecular Cell 41:733-746.

DRSC at ADRC

2011-03-17T09:58:00.009-04:00

The DRSC will be represented at the fly meeting this year by myself (S. Mohr, DRSC Director) and bioinformatician Claire Hu.

Please feel free to email me if you'd like to set up a time to meet for a confidential talk about your screening plans.

I will also be presenting in the Techniques and Genomics session (Platform #133, Mohr et al. Application of High-Content Imaging to Genome-Scale Interrogations of the Nucleus).

Claire will be presenting a poster in the human disease category on identification of orthologs of fly genes and matching fly genes to human diseases (Poster #452B, Hu et al. DIOPT, the DRSC Integrative Ortholog Prediction Tool). Please drop by and welcome Claire to her first fly conference!

The Transgenic RNAi Project (TRiP) will also be represented at the meeting. Check out back-to-back posters #952A and 951C to see what's new with the in vivo side of things.

Breaking Report: Small-Scale ER Screen

2011-03-14T10:16:00.006-04:00

On my desk to read today? A targeted screen looking at 156 putative ER proteins identified bioinformatically and then studied in a cell-based microscopy assay.

Kondylis et al. (2011) Identification of ER proteins involved in the functional organisation of the early secretory pathway in Drosophila cells by a targeted RNAi screen. PLoS ONE. Open Access. Protocol Note: Screened in S2 cells.

Interested to do a similar screen--one targeted to a small sub-set of genes? The DRSC is filling requests for custom library production based on our collection of more than 30,000 high-quality amplicons. Please contact the director for more information.

Breaking Report: Power of Combinatorial RNAi

2011-03-08T10:39:00.004-05:00

On my desk to read today? A new report from T. Horn and colleagues in the Boutros group on the use of double-knockdown to uncover genetic interactions.

Horn et al. (2011) Mapping of signaling networks through synthetic genetic interaction analysis by RNAi. Nature Methods. Advanced online publication. PMID: 21378980.

More than 70,000 measurements!

Breaking Report: Ricin Resistance & Sensitivity

2011-03-03T10:01:00.006-05:00

On my desk to read today? A breaking report of an RNAi screen for resistance and sensitivity to the plant toxin ricin.

Pawar et al. (2011) RNAi Screening of Drosophila (Sophophora) melanogaster S2 Cells for Ricin Sensitivity and Resistance. Journal of Biomolecular Screening. DOI: 10.1177/1087057110397890

Breaking Report: Ras/MAPK signaling and Immune Responses

2011-02-23T10:40:00.002-05:00

On my desk to read today? A breaking report from the Boutros lab.

Ragab et al. (2011) Drosophila Ras/MAPK signalling regulates innate immune responses in immune and intestinal stem cells. EMBO J. 2011 Feb 4. Protocol Note: screened in SL2 cells with follow-up in vivo using RNAi and mutant strains.

Breaking Report

2011-02-18T11:27:00.003-05:00

On my desk today? A new report that uses RNAi in the study (and based their designs on DRSC amplicon designs).

Chan et al. (2011) Expanded polyglutamine domain possesses nuclear export activity which modulates subcellular localization and toxicity of polyQ disease protein via exportin-1. Hum. Mol. Genet.

Meeting Announcement

2011-02-18T11:24:00.002-05:00

Recently came across a meeting announcement I will pass along:

6th International Symposium on Molecular Insect Science, October 2-5, 2011, Amsterdam, The Netherlands. More information at their website.

Be Ever-Vigilant!

2011-01-31T10:52:00.002-05:00

On my desk to read today?

Sigoillot and King (2011) Vigilance and Validation: Keys to Success in RNAi Screening. ACS Chem Biol. 2011 6(1):47-60.

Breaking Report: Living Cell Microarray Screen

2011-01-25T09:48:00.002-05:00

On my desk to read this morning?

Linquist et al. (2011) Genome-scale RNAi on living-cell microarrays identifies novel regulators of Drosophila melanogaster TORC1-S6K pathway signaling. Genome Research. PMID: 21239477.

False Discovery--Real Publication

2011-01-20T09:29:00.005-05:00

Excited to see that a publication from the DRSC is now available online:

Booker et al. (2011) False negative rates in Drosophila cell-based RNAi screens: A case study. BMC Genomicsw 12:50. Open Access.

Breaking Report: Sweet Relief?

2011-01-05T12:59:00.003-05:00

Also on my desk today? A report describing the application of RNAi in the field--an effort to address honeybee colony collapse disorder.

Hunter et al. (2010) Large-Scale Field Application of RNAi Technology Reducing Israeli Acute Paralysis Virus Disease in Honey Bees (Apismellifera, Hymenoptera: Apidae). PLoS Pathogens. Open Access.

The authors note that "To our knowledge, this is the first successful large-scale real world use of RNAi for disease control."

Breaking Reports: Screen & Review

2011-01-05T10:03:00.003-05:00

On my desk to read, early in this new year? Two papers from our near neighbors in the Perrimon lab.

Neumüller and Perrimon (2010) Where gene discovery turns into systems biology: genome-scale RNAi screens in Drosophila. Wiley Interdiscip Rev Syst Biol Med. 2010 Dec 31.

Kondo and Perrimon (2011) A Genome-Wide RNAi Screen Identifies Core Components of the G2-M DNA Damage Checkpoint. Sci. Signal. Jan 4. Vol. 4, Issue 154, p. rs1. Note: Screen performed at the DRSC.

Breaking Reports: Cell-Based Screens

2010-12-17T14:20:00.004-05:00

Catching up on my reading today. On the list:

Asensio et al. (2010) RNAi screen identifies a role for adaptor protein AP-3 in sorting to the regulated secretory pathway. J Cell Biol. 2010 Dec 13;191(6):1173-87. Protocol Notes: Screened in S2 cells using a library of "7,216 sequences that target Drosophila genes conserved to mammals."

Grimberg et al. (2010) Basic-Leucine Zipper Protein Cnc-C is a Substrate and Transcriptional Regulator of the Drosophila 26S Proteasome. Mol Cell Biol. Dec 13. Epub ahead of print. Protocol Notes: Screened the DRSC Transcription Factor library.

Primary Cells

2010-12-06T10:00:00.002-05:00

On my desk today? A report that uses RNAi and primary cells to study muscles.

Rui et al. (2010) Sarcomere formation occurs by the assembly of multiple latent protein complexes. PLoS Genet. 6(11):e1001208.

Nominate Genes for TRiP Stock Production

2010-12-01T16:04:00.007-05:00

The Trangenic RNAi Project (TRiP) is still taking community nominations for genes to go into the production pipeline for in vivo TRiP RNAi stocks. Nominate!

See the bottom of this page for the contact email for nomination:

http://www.flyrnai.org/TRiP-ACC-OVR.html

Ouch! That's hot.

2010-11-22T11:01:00.006-05:00

On my desk today? Report of an in vivo screen for genes involved in heat avoidance.

Neely et al. (2010) A genome-wide Drosophila screen for heat nociception identifies alpha-2-delta-3 as an evolutionarily conserved pain gene. Cell 143(4):628-38. PMID: 21074052

Breaking Reports: Full-Genome RNAi on cell spreading & a Library Evaluation

2010-11-09T08:27:00.003-05:00

On my desk today? Catching up on breaking reports from two different groups--one is a full-genome cell-based RNAi screen and the other a comparative report on genome-wide libraries.

D'Ambrosio & Vale (2010) A whole genome RNAi screen of Drosophila S2 cell spreading performed using automated computational image analysis. J Cell Bio 191(3):471-8. PMID: 21041442.

Horn et al. (2010) Design and evaluation of genome-wide libraries for RNA interference screens. Genome Biol. 11(6):R61. PMID 20550664.

Web Wednesday: RNAi Select

2010-10-27T08:55:00.003-04:00

Following up on a recent post--breaking paper on dsRNA design--here's the link to the tool reported in the paper.

http://www.rnaiselect.info/dsrna/

Breaking Report: piRNAs

2010-10-25T15:21:00.002-04:00

On my desk to read today? A report on the RNA biology of piRNAs, that includes work using dsRNA-based knockdown of piwi in cultured cells.

Haase et al. (2010) Probing the initiation and effector phases of the somatic piRNA pathway in Drosophila. Genes Dev. 2010 Oct 21. [Epub ahead of print]

Breaking Report: Limiting Off-Target Effects

2010-10-22T10:10:00.003-04:00

Also on my desk today? An informatics analysis and tool for further limiting potential off-target effects in dsRNA design.

Seinen et al. (2010) RNAi Experiments in D. melanogaster: Solutions to the Overlooked Problem of Off-Targets Shared by Independent dsRNAs. PLoS One. 2010 Oct 1;5(10). pii: e13119.

Breaking Report: DRSC screen for modifiers of Notch transcriptional activity

2010-10-22T10:06:00.004-04:00

On my desk today? A report of a screen performed using the DRSC full-genome library.

Mourikis et al. (2010) Modifiers of notch transcriptional activity identified by genome-wide RNAi. BMC Developmental Biology. http://www.biomedcentral.com/1471-213X/10/107

Breaking Report: Myc study points to dHCF

2010-10-18T10:09:00.003-04:00

Also on my desk today? Another cell-based RNAi screen report, this one looking at activation of Myc target genes.

Furrer et al. (2010) Drosophila Myc interacts with Host Cell Factor (dHCF) to activate transcription and control growth. J Biol Chem. 2010 Oct 11. [Epub ahead of print]

Breaking Report: Splicing mapk

2010-10-18T09:56:00.002-04:00

What's on my desk to read today? A breaking report by Ashton-Beaucage et al. that includes cell-based RNAi screening and in vivo RNAi screening as follow-up.

Ashton-Beaucage et al. (2010) The exon junction complex controls the splicing of MAPK and other long intron-containing transcripts in Drosophila. Cell. 2010 Oct 15;143(2):251-62.

Recent Review: miRNAs & Cancer

2010-10-14T11:46:00.004-04:00

What's on my desk to read today? A recent review on miRNAs and cancer.

This review is not directly relevant to using RNAi for screens, of course. But Fig. 4 is a nice summary of tools for disrupting miRNAs. And I like to try to keep up with aspects of RNA biology, as understanding RNA biology is interlinked with exploiting it as a research tool.

Garzon et al. (2010) Targeting microRNAs in cancer: rationale, strategies and challenges. Nature Reviews Drug Discovery 9: 775-789. Available FREE.

Breaking Report: Flight

2010-10-06T15:30:00.002-04:00

On my desk today? A new report on the Flight database.

Sims et al. (2010) The flight Drosophila RNAi database: 2010 update. Fly (Austin). 2010 Oct 10;4(4).

Travel Grants for Interdisciplinary Collaborations

2010-09-28T14:21:00.002-04:00

Just saw this announced: Burrows Welcome Fund Collaborative Research Travel Grant.

From their website: "This program provides ... support for researchers ... to travel ... to a laboratory to acquire a new research technique, to facilitate/begin collaboration, or to attend a course. Applicants must hold a Ph.D. or are studying for a Ph.D. in mathematics, physics, chemistry, computer science, statistics, or engineering who are interested in investigating research opportunities in the biological sciences or to biologists interested in working with physical scientists, mathematicians, engineers, chemists, statisticians, or computer scientists to incorporate their ideas and approaches to answering biological questions."

SILAC & RNAi

2010-09-21T13:19:00.004-04:00

Also on my desk today? A chapter with protocols on combining SILAC-labeling and mass spec with RNAi in Drosophila cultured cells.

Cuomo and Bonaldi (2010) Systems Biology “On-the-Fly”: SILAC-Based Quantitative Proteomics and RNAi Approach in Drosophila melanogaster. Methods Mol Biol. 662:59-78.

Breaking Report: Jak/Stat

2010-09-21T10:09:00.002-04:00

What's on my desk to read today? A report that includes screening of a focused set of 67 candidate genes in Kc cells.

Vidal et al. (2010) Negative regulation of Drosophila JAK-STAT signalling by endocytic trafficking. J Cell Sci. 2010 Sep 14. [Epub ahead of print]

New on the DRSC Website

2010-09-17T09:19:00.003-04:00

We've just added a map showing empty and control wells on an example plate from the Kinases & Phosphatases set on the sub-libraries web page. For 'the subs' we leave empty wells around the edges to minimize the potential impact of edge-effects on experimental data.

Meeting Announcement

2010-09-16T13:15:00.002-04:00

Just received an announcement for the 5th Annual Arthropod Genomics Symposium, June 9 to 12, 2011, Kansas City Marriott on the beautiful Country Club Plaza.

Methods Video

2010-09-15T16:19:00.005-04:00

What am I watching today? A new video on fly RNAi methods.

Moser et al. (2010) RNAi Screening for Host Factors Involved in Vaccinia Virus Infection using Drosophila Cells. J Vis Exp. 2010 Aug 25;(42). pii: 2137. doi: 10.3791/2137.

Just the Facts, Please

2010-09-13T14:44:00.004-04:00

We've just updated our Assay Overview page, which describes the instruments available at the DRSC (or at collaborating facilities) for high-content imaging, plate-reader, etc. screens. It's not beautiful design but we hope it gives the information folks need.

Breaking Report: Wound Closure

2010-09-08T11:56:00.002-04:00

What's on my desk today? A screen of ~200 in vivo RNAi lines from the VDRC & NIG-Fly collections to identify genes involved in wound closure.

Lesch et al. (2010) A Targeted UAS-RNAi Screen in Drosophila Larvae Identifies Wound Closure Genes Regulating Distinct Cellular Processes. in Genetics.

Presentation on in-cell in situ at HMS

2010-09-07T08:55:00.004-04:00

Are you local? The ICCB-Longwood Screening Facility is hosting a workshop on in situ in cells (the Quantigene ViewRNA technology from Affymetrix). See the ICCB-L website for details.

Live Cell Imaging Analysis

2010-08-31T11:16:00.003-04:00

What's on my desk today? A report on a new open source software package for analysis of high-throughput live cell images.

Held et al. (2010) CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging. Nature Methods. 7, 747–754.

Quote of the Week: Technology

2010-08-27T09:03:00.004-04:00

Quote of of the summer, at this point? It's been a while!

My hypodermic syringe is of the simplest. It consists of a little glass tube, tapering sharply at one end. By drawing in my breath, I fill it with the liquid to be tested; I expel the contents by blowing. Its point is almost as fine as a hair and enables me to regulate the dose to the degree which I want. A cubic millimetre is the usual charge. The injection has to be made at parts that are generally covered with horn. So as not to break the point of my fragile instrument, I prepare the way with a needle, with which I prick the victim at the spot required. I insert the tip of the loaded injector in the hole thus made and I blow. The thing is done in a moment, very neatly and in an orthodox fashion, favourable to delicate experiments. I am delighted with my modest apparatus.

from The Life of the Fly by J.H. Fabre, translated by A. Teixeira de Mattos

(1913, Dodd, Mead & Co., NY)