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1.  A genome-scale shRNA resource for transgenic RNAi in Drosophila 
Nature methods  2011;8(5):405-407.
Existing transgenic RNAi resources in Drosophila melanogaster based on long double-stranded hairpin RNAs are powerful tools for functional studies, but they are ineffective in gene knockdown during oogenesis, an important model system for the study of many biological questions. We show that shRNAs, modeled on an endogenous microRNA, are extremely effective at silencing gene expression during oogenesis. We also describe our progress toward building a genome-wide shRNA resource.
doi:10.1038/nmeth.1592
PMCID: PMC3489273  PMID: 21460824
2.  FlyRNAi.org—the database of the Drosophila RNAi screening center: 2012 update 
Nucleic Acids Research  2011;40(D1):D715-D719.
FlyRNAi (http://www.flyrnai.org), the database and website of the Drosophila RNAi Screening Center (DRSC) at Harvard Medical School, serves a dual role, tracking both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. The database and website is used as a platform for community availability of protocols, tools, and other resources useful to researchers planning, conducting, analyzing or interpreting the results of Drosophila RNAi screens. Based on our own experience and user feedback, we have made several changes. Specifically, we have restructured the database to accommodate new types of reagents; added information about new RNAi libraries and other reagents; updated the user interface and website; and added new tools of use to the Drosophila community and others. Overall, the result is a more useful, flexible and comprehensive website and database.
doi:10.1093/nar/gkr953
PMCID: PMC3245182  PMID: 22067456
3.  False negative rates in Drosophila cell-based RNAi screens: a case study 
BMC Genomics  2011;12:50.
Background
High-throughput screening using RNAi is a powerful gene discovery method but is often complicated by false positive and false negative results. Whereas false positive results associated with RNAi reagents has been a matter of extensive study, the issue of false negatives has received less attention.
Results
We performed a meta-analysis of several genome-wide, cell-based Drosophila RNAi screens, together with a more focused RNAi screen, and conclude that the rate of false negative results is at least 8%. Further, we demonstrate how knowledge of the cell transcriptome can be used to resolve ambiguous results and how the number of false negative results can be reduced by using multiple, independently-tested RNAi reagents per gene.
Conclusions
RNAi reagents that target the same gene do not always yield consistent results due to false positives and weak or ineffective reagents. False positive results can be partially minimized by filtering with transcriptome data. RNAi libraries with multiple reagents per gene also reduce false positive and false negative outcomes when inconsistent results are disambiguated carefully.
doi:10.1186/1471-2164-12-50
PMCID: PMC3036618  PMID: 21251254
4.  Stevens-Johnson Syndrome triggered by chemical hair relaxer: a case report 
Cases Journal  2009;2:7748.
This case report describes a 41-year-old Afro-Caribbean lady presenting with a constellation of pyrexia, conjunctivitis, arthralgia, sterile dysuria, apthous ulceration, labial crusting and widespread erythema multiforme. A diagnosis of Stevens-Johnson Syndrome was made. She had taken no medications recently (the most common precipitant of Stevens-Johnson Syndrome) and a full screen for the common and atypical bacterial and viral triggers was negative. The identified trigger was the use of a chemical hair relaxant treatment a few days previously. With supportive measures and a course of oral prednisolone, the patient quickly improved and made a full recovery. This case highlights the importance of considering occupational and recreational precipitants of Stevens-Johnson Syndrome.
doi:10.4076/1757-1626-2-7748
PMCID: PMC2769367  PMID: 19918477
5.  Aseptic meningitis in a patient taking etanercept for rheumatoid arthritis: a case report 
Cases Journal  2008;1:364.
Background
We report a case of a 53 year old lady recently commenced on etanercept, an anti-TNF (tumour necrosis factor) therapy for rheumatoid arthritis presenting with confusion, pyrexia and an erythematous rash.
Case presentation
A lumbar puncture was highly suggestive of bacterial meningitis, but CSF cultures produced no growth, and polymerase chain reactions (PCR) for all previously reported bacterial, fungal and viral causes of meningitis were negative.
Conclusion
This case report describes aseptic meningitis as a previously unreported complication of etanercept therapy, and serves as a reminder of the rare but potentially life-threatening risk of serious infections in patients taking anti-TNF therapy for a variety of conditions.
doi:10.1186/1757-1626-1-364
PMCID: PMC2612655  PMID: 19046446
6.  Neurocysticercosis as a first presentation of tonic-clonic seizures: a case report 
Cases Journal  2008;1:104.
We report the case of a 28 year-old immigrant Asian man from the Punjab region with a first presentation of seizures. This patient had no significant past medical history, but suffered several headaches in the preceding week and was pyrexial on presentation. A CT scan of his head showed a single area of subcortical low attenuation initially suggesting ischaemia. A lumbar puncture and CSF examination was unremarkable. Further investigation revealed discrete calcified gluteal lesions on pelvic X-ray, and serum immunology positive for cysticercosis. The diagnosis of neurocysticercosis was made, and the patient improved on dexamethasone and a short course of vermicide, to be discharged a week later. With increasing global migration, the prevalence of neurological parasitic infections seen in the UK is likely to rise. This case highlights the importance of careful interpretation of non-specific head CTs in the context of first presentation of seizures in a susceptible population.
doi:10.1186/1757-1626-1-104
PMCID: PMC2531088  PMID: 18710554
7.  Vector and parameters for targeted transgenic RNA interference in Drosophila melanogaster 
Nature methods  2007;5(1):49-51.
The conditional expression of hairpin constructs in Drosophila melanogaster has emerged in recent years as a method of choice in functional genomic studies. To date, upstream activating site–driven RNA interference constructs have been inserted into the genome randomly using P-element–mediated transformation, which can result in false negatives due to variable expression. To avoid this problem, we have developed a transgenic RNA interference vector based on the phiC31 site-specific integration method.
doi:10.1038/nmeth1146
PMCID: PMC2290002  PMID: 18084299
8.  A case study of the reproducibility of transcriptional reporter cell-based RNAi screens in Drosophila 
Genome Biology  2007;8(9):R203.
A second generation dsRNA library was used to re-assess factors that influence the outcome of transcriptional reporter-based whole-genome RNAi screens for the Wnt/Wingless (wg) and Hedgehog (hh)-signaling pathways.
Off-target effects have been demonstrated to be a major source of false-positives in RNA interference (RNAi) high-throughput screens. In this study, we re-assess the previously published transcriptional reporter-based whole-genome RNAi screens for the Wingless and Hedgehog signaling pathways using second generation double-stranded RNA libraries. Furthermore, we investigate other factors that may influence the outcome of such screens, including cell-type specificity, robustness of reporters, and assay normalization, which determine the efficacy of RNAi-knockdown of target genes.
doi:10.1186/gb-2007-8-9-r203
PMCID: PMC2375041  PMID: 17903264
9.  FlyRNAi: the Drosophila RNAi screening center database 
Nucleic Acids Research  2005;34(Database issue):D489-D494.
RNA interference (RNAi) has become a powerful tool for genetic screening in Drosophila. At the Drosophila RNAi Screening Center (DRSC), we are using a library of over 21 000 double-stranded RNAs targeting known and predicted genes in Drosophila. This library is available for the use of visiting scientists wishing to perform full-genome RNAi screens. The data generated from these screens are collected in the DRSC database () in a flexible format for the convenience of the scientist and for archiving data. The long-term goal of this database is to provide annotations for as many of the uncharacterized genes in Drosophila as possible. Data from published screens are available to the public through a highly configurable interface that allows detailed examination of the data and provides access to a number of other databases and bioinformatics tools.
doi:10.1093/nar/gkj114
PMCID: PMC1347476  PMID: 16381918

Results 1-9 (9)