FlyRNAi.org-the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update.

The FlyRNAi database of the Drosophila RNAi Screening Center (DRSC) and Transgenic RNAi Project (TRiP) at Harvard Medical School and associated DRSC/TRiP Functional Genomics Resources website (http://fgr.hms.harvard.

The Transgenic RNAi Project at Harvard Medical School: Resources and Validation.

To facilitate large-scale functional studies in Drosophila, the Drosophila Transgenic RNAi Project (TRiP) at Harvard Medical School (HMS) was established along with several goals: developing efficient vectors for RNAi that work in all tissues, generating a genome-scale collection of RNAi stocks with input from the community, distributing the lines as they are generated through existing stock centers, validating as many lines as possible using RT-qPCR and phenotypic analyses, and developing tools and web resources for identifying RNAi lines and retrieving existing information on their quality. With these goals in mind, here we describe in detail the various tools we developed and the status of the collection, which is currently composed of 11,491 lines and covering 71% of Drosophila genes. Data on the characterization of the lines either by RT-qPCR or phenotype is available on a dedicated website, the RNAi Stock Validation and Phenotypes Project (RSVP, http://www.

FlyPrimerBank: an online database for Drosophila melanogaster gene expression analysis and knockdown evaluation of RNAi reagents.

The evaluation of specific endogenous transcript levels is important for understanding transcriptional regulation. More specifically, it is useful for independent confirmation of results obtained by the use of microarray analysis or RNA-seq and for evaluating RNA interference (RNAi)-mediated gene knockdown. Designing specific and effective primers for high-quality, moderate-throughput evaluation of transcript levels, i.

UP-TORR: online tool for accurate and Up-to-Date annotation of RNAi Reagents.

RNA interference (RNAi) is a widely adopted tool for loss-of-function studies but RNAi results only have biological relevance if the reagents are appropriately mapped to genes. Several groups have designed and generated RNAi reagent libraries for studies in cells or in vivo for Drosophila and other species. At first glance, matching RNAi reagents to genes appears to be a simple problem, as each reagent is typically designed to target a single gene.

FlyRNAi.org--the database of the Drosophila RNAi screening center: 2012 update.

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.

An integrative approach to ortholog prediction for disease-focused and other functional studies.

Background: Mapping of orthologous genes among species serves an important role in functional genomics by allowing researchers to develop hypotheses about gene function in one species based on what is known about the functions of orthologs in other species. Several tools for predicting orthologous gene relationships are available. However, these tools can give different results and identification of predicted orthologs is not always straightforward.

False negative rates in Drosophila cell-based RNAi screens: a case study.

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%.

Design and implementation of high-throughput RNAi screens in cultured Drosophila cells.

This protocol describes the various steps and considerations involved in planning and carrying out RNA interference (RNAi) genome-wide screens in cultured Drosophila cells. We focus largely on the procedures that have been modified as a result of our experience over the past 3 years and of our better understanding of the underlying technology. Specifically, our protocol offers a set of suggestions and considerations for screen optimization and a step-by-step description of the procedures successfully used at the Drosophila RNAi Screening Center for screen implementation, data collection and analysis to identify potential hits.

FlyRNAi: the Drosophila RNAi screening center database.

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.

Effects of dexpanthenol with or without Aloe vera extract on radiation-induced oral mucositis: preclinical studies.

Purpose: To define the effect of dexpanthenol with or without Aloe vera extract on radiation-induced oral mucositis.

Materials And Methods: Mouse tongue mucosal ulceration was analysed as the clinically relevant endpoint. Graded single or fractionated dose irradiation (10 x 3 Gy/2 weeks, graded test doses on day 14) were combined with topical administration of dexpanthenol or a base, with or without Aloe vera extract.

Modulation of the cell kinetics of pig skin by the topical application of evening primrose oil or Lioxasol.

The daily topical application of two compounds, a cream containing 10% evening primrose oil (EPO) and Lioxasol (a compound used clinically to treat radiation burns), resulted in increased cell proliferative activity in the skin of female Large White pigs. The effect was most pronounced in the case of the EPO based cream, and was comparable in magnitude with that observed in a previous study on pig skin using orally administered EPO. There was an increase in the size of the rete pegs in the epidermis by 6 weeks after the start of application of the EPO cream.

Assessment of an in situ rat intestine preparation with perfused vascular bed for studying the absorption and first-pass metabolism of drugs.

The perfused in situ rat jejunum preparation originally described by Hanson and Parsons (1976) was adapted for use in absorption and metabolism studies with drugs. The preparation allows simultaneous perfusion of the gut lumen and associated vasculature and is viable for one hour. The viability of the preparation was assessed, and the application of the method is illustrated by experiments with the opiate analgesic, buprenorphine.

Effects of idazoxan on catecholamine systems in rat brain.

Experiments have been performed to assess the potency of idazoxan (RX 781094) at alpha and beta-adrenoceptors and dopamine receptors and on catecholamine uptake processes in rat brain. The effects of idazoxan on the turnover rates of noradrenaline and dopamine have been determined. Radioligand binding studies with cerebral cortex membranes have demonstrated that idazoxan exhibits 46-fold selectivity for alpha 2-adrenoceptors labelled by (3H)-idazoxan (Mean Ki +/- S.

The radioimmunoassay of buprenorphine.

Antisera to buprenorphine were obtained in rabbits immunised with 3-0-carboxymethylbuprenorphine and N-hemisuccinyl-norbuprenorphine conjugated to bovine serum albumin. Using the latter antiserum and tritium labelled buprenorphine a radioimmunoassay have good accuracy and precision was developed for concentrations as low as 50 picograms in 1 ml of plasma. The N-hemisuccinyl antiserum crossreacted with norbuprenorphine, and the 3-0-glucuronide conjugate with the 3-0-carboxymethyl antiserum.

Structure-activity relationships in the development of hypoxic cell radiosensitizers. I. Sensitization efficiency.

The efficiency of 35 nitroaromatic and nitroheterocyclic compounds in radiosensitizing hypoxic Chinese Hamster cells in vitro was determined. The concentration C of the compound required to achieve an enhancement ratio of 1.6 was measured, and the redox and partition properties were quantified as the one-electron reduction potential at pH 7, E, and the octanol: water partition coefficient, P, respectively.

Some aspects of the metabolism of misonidazole.

The metabolism of the 2-nitroimidazole hypoxic cell radiosensitizer, misonidazole, has been studied in patients receiving radiotherapy. Results are presented which show that the compound reaches adequate levels in tumour tissue and that, in animal systems, reduction products of the nitro group may also be present. Ah h.

The rationale for the development of improved hypoxic cell radiosensitizers.

This paper outlines the chemical background to the selection of compounds likely to be clinically superior to the nitroimidazoles currently being evaluated in cancer therapy. The most important chemical properties to consider are electron affinity and lipophilicity, and the quantification and prediction of both these properties are considered. Examples are presented of the use of multiple regression analysis to evaluate the relative contribution of individual properties to the overall biological response.

The optimum regime for the administration of misonidazole and the establishment of multi-centre clinical trials.

The amount of misonidazole which may be given to one patient is limited because of the risk of neurotoxicity. The drug may be given with every treatment of a multi-fraction course of radiotherapy or only with some of the treatments. The number of radiotherapy treatments can be reduced or multiple treatments given after each dose of the drug.

The neurotoxicity of misonidazole and its relationship to dose, half-life and concentration in the serum.

Misonidazole has been given to a total of 87 patients. Neurotoxicity has occurred--convulsions with the higher doses and peripheral neuropathy with the lowern ones. The data from 34 patients receiving 4--7 doses has been analysed.