E-RNAi: a web application to design optimized RNAi constructs

RNA interference (RNAi) has become a powerful genetic approach to systematically dissect gene function on a genome-wide scale. Owing to the penetrance and efficiency of RNAi in invertebrates, model organisms such as Drosophila melanogaster and Caenorhabditis elegans have contributed significantly to the identification of novel components of diverse biological pathways, ranging from early development to fat storage and aging. For the correct assessment of phenotypes, a key issue remains the stringent quality control of long double-stranded RNAs (dsRNA) to calculate potential off-target effects that may obscure the phenotypic data. We here describe a web-based tool to evaluate and design optimized dsRNA constructs. Moreover, the application also gives access to published predesigned dsRNAs. The E-RNAi web application is available at

Electrocardiographic findings of carbon monoxide intoxication; two cases

IntroductionCarbon monoxide (CO) poisoning is a life threatening emergency. Oxygen delivery to tissues is reduced and hypoxia develops. Most affected systems are the central nervous system and cardiovascular system. For the diagnosis of CO poisoning, first poisoning should be suspected and then blood carboxyhaemoglobin (COHb) levels should be measured. For cardiovascular evaluation ECG is required.Case 1A 56-year-old male patient admitted to ED with complaints of syncope, headache, dizziness and blurred vision. Patient was mentally confused and on ECG sinus tachycardia was present (Fig. 1). On blood gas analysis COHb value was measured 33.3%. Due to syncope and ECG changes hyperbaric oxygen (HBO) therapy initiated. After the treatment, COHb value was measured 4.5% and ECG showed normal sinus rhythm. Patient was discharged with recommendations.Case 2An unconscious 36-year-old female patient admitted to ED with a diagnosis of CO poisoning. ECG revealed ST depression on DII-DIII-AVF leads (Fig. 2) and elevated troponin I (0.1ng/ml) and CK-MB (47U/L) values were determined. On blood gas analysis, COHb value was measured 39.8%. HBO therapy initiated. After HBO therapy patient was conscious and for further follow-up patient was admitted to intensive care unit.Discussion and ConclusionAlthough there is no classic ”carbon monoxide” ECG pattern, sinus tachycardia and ST-T depressions are the most common ECG findings. Even a small amount of exposure to CO can cause myocardial infarction, especially in patients with coronary artery disease. Patients admitting to ED with chest pain and ECG changes may be considered as a possible CO poisoning and patients with CO poisoning must be carefully evaluated for cardiovascular disease

GenomeRNAi: a database for cell-based RNAi phenotypes

RNA interference (RNAi) has emerged as a powerful tool to generate loss-of-function phenotypes in a variety of organisms. Combined with the sequence information of almost completely annotated genomes, RNAi technologies have opened new avenues to conduct systematic genetic screens for every annotated gene in the genome. As increasing large datasets of RNAi-induced phenotypes become available, an important challenge remains the systematic integration and annotation of functional information. Genome-wide RNAi screens have been performed both in Caenorhabditis elegans and Drosophila for a variety of phenotypes and several RNAi libraries have become available to assess phenotypes for almost every gene in the genome. These screens were performed using different types of assays from visible phenotypes to focused transcriptional readouts and provide a rich data source for functional annotation across different species. The GenomeRNAi database provides access to published RNAi phenotypes obtained from cell-based screens and maps them to their genomic locus, including possible non-specific regions. The database also gives access to sequence information of RNAi probes used in various screens. It can be searched by phenotype, by gene, by RNAi probe or by sequence and is accessible a

Effectiveness of floating micro-bead bio-filter for ornamental fish in a re-circulating aquaculture system.

Bio-filtration has been widely used in re-circulating aquaculture system to remove waste and to convert toxic ammonia and nitrite into safe end products ornamental fish and other aquatic organisms. However, the study of micro-bead usage as the filter medium has not yet been broadened and thoroughly developed. Therefore, the aim of this study is to construct a biological filter made from polyethylene micro-bead as the filter medium and to analyze its effectiveness in removing waste as well as in converting the toxic organic matter into stable substances. The bio-filter was constructed under a rotational molding process. The tubes, hoses, and piping were made from polyvinyl chloride (PVC) while the fasteners were made from stainless steel and other non-corrosive materials. The effectiveness of this bio-filter was measured by using biochemical oxygen demand (BOD) and total suspended solids (TSS) analysis. Results indicated that this bio-filter is efficient enough to remove suspended solids and BOD. Therefore, this floating micro-bead bio-filter can be used in aquaculture systems

RNAiAtlas: a database for RNAi (siRNA) libraries and their specificity

Large-scale RNA interference (RNAi) experiments, especially the ones based on short-interfering RNA (siRNA) technology became increasingly popular over the past years. For such knock-down/screening purposes, different companies offer sets of oligos/reagents targeting the whole genome or a subset of it for various organisms. Obviously, the sequence (and structure) of the corresponding oligos is a key factor in obtaining reliable results in these large-scale studies and the companies use a variety of (often not fully public) algorithms to design them. Nevertheless, as the genome annotations are still continuously changing, oligos may become obsolete, so siRNA reagents should be periodically re-annotated according to the latest version of the sequence database (which of course has serious consequences also on the interpretation of the screening results). In our article, we would like to introduce a new software/database tool, the RNAiAtlas. It has been created for exploration, analysis and distribution of large scale RNAi libraries (currently limited to the human genome) with their latest annotation (including former history) but in addition it contains also specific on-target analysis results (design quality, side effects, off-targets)

Effectiveness of Floating Micro-Bead Bio-Filter for Ornamental Fish in a Re-Circulating Aquaculture System

Abstract Bio-filtration has been widely used in re-circulating aquaculture system to remove waste and to convert toxic ammonia and nitrite into safe end products ornamental fish and other aquatic organisms. However, the study of micro-bead usage as the filter medium has not yet been broadened and thoroughly developed. Therefore, the aim of this study is to construct a biological filter made from polyethylene micro-bead as the filter medium and to analyze its effectiveness in removing waste as well as in converting the toxic organic matter into stable substances. The bio-filter was constructed under a rotational molding process. The tubes, hoses, and piping were made from polyvinyl chloride (PVC) while the fasteners were made from stainless steel and other non-corrosive materials. The effectiveness of this bio-filter was measured by using biochemical oxygen demand (BOD) and total suspended solids (TSS) analysis. Results indicated that this bio-filter is efficient enough to remove suspended solids and BOD. Therefore, this floating micro-bead bio-filter can be used in aquaculture systems

E-RNAi: a web application for the multi-species design of RNAi reagents—2010 update

The design of RNA interference (RNAi) reagents is an essential step for performing loss-of-function studies in many experimental systems. The availability of sequenced and annotated genomes greatly facilitates RNAi experiments in an increasing number of organisms that were previously not genetically tractable. The E-RNAi web-service, accessible at http://www.e-rnai.org/, provides a computational resource for the optimized design and evaluation of RNAi reagents. The 2010 update of E-RNAi now covers 12 genomes, including Drosophila, Caenorhabditis elegans, human, emerging model organisms such as Schmidtea mediterranea and Acyrthosiphon pisum, as well as the medically relevant vectors Anopheles gambiae and Aedes aegypti. The web service calculates RNAi reagents based on the input of target sequences, sequence identifiers or by visual selection of target regions through a genome browser interface. It identifies optimized RNAi target-sites by ranking sequences according to their predicted specificity, efficiency and complexity. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design. Results are presented online, as a downloadable HTML report and as tab-delimited files

A novel method for tissue-specific RNAi rescue in Drosophila

Targeted gene silencing by RNA interference allows the study of gene function in plants and animals. In cell culture and small animal models, genetic screens can be performed—even tissue-specifically in Drosophila—with genome-wide RNAi libraries. However, a major problem with the use of RNAi approaches is the unavoidable false-positive error caused by off-target effects. Until now, this is minimized by computational RNAi design, comparing RNAi to the mutant phenotype if known, and rescue with a presumed ortholog. The ultimate proof of specificity would be to restore expression of the same gene product in vivo. Here, we present a simple and efficient method to rescue the RNAi-mediated knockdown of two independent genes in Drosophila. By exploiting the degenerate genetic code, we generated Drosophila RNAi Escape Strategy Construct (RESC) rescue proteins containing frequent silent mismatches in the complete RNAi target sequence. RESC products were no longer efficiently silenced by RNAi in cell culture and in vivo. As a proof of principle, we rescue the RNAi-induced loss of function phenotype of the eye color gene white and tracheal defects caused by the knockdown of the heparan sulfate proteoglycan syndecan. Our data suggest that RESC is widely applicable to rescue and validate ubiquitous or tissue-specific RNAi and to perform protein structure–function analysis

GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update

The GenomeRNAi database (http://www.genomernai.org/) contains phenotypes from published cell-based RNA interference (RNAi) screens in Drosophila and Homo sapiens. The database connects observed phenotypes with annotations of targeted genes and information about the RNAi reagent used for the perturbation experiment. The availability of phenotypes from Drosophila and human screens also allows for phenotype searches across species. Besides reporting quantitative data from genome-scale screens, the new release of GenomeRNAi also enables reporting of data from microscopy experiments and curated phenotypes from published screens. In addition, the database provides an updated resource of RNAi reagents and their predicted quality that are available for the Drosophila and the human genome. The new version also facilitates the integration with other genomic data sets and contains expression profiling (RNA-Seq) data for several cell lines commonly used in RNAi experiments

RNAi Screening in Drosophila Cells Identifies New Modifiers of Mutant Huntingtin Aggregation

The fruitfly Drosophila melanogaster is well established as a model system in the study of human neurodegenerative diseases. Utilizing RNAi, we have carried out a high-throughput screen for modifiers of aggregate formation in Drosophila larval CNS-derived cells expressing mutant human Huntingtin exon 1 fused to EGFP with an expanded polyglutamine repeat (62Q). 7200 genes, encompassing around 50% of the Drosophila genome, were screened, resulting in the identification of 404 candidates that either suppress or enhance aggregation. These candidates were subjected to secondary screening in normal length (18Q)-expressing cells and pruned to remove dsRNAs with greater than 10 off-target effects (OTEs). De novo RNAi probes were designed and synthesized for the remaining 68 candidates. Following a tertiary round of screening, 21 high confidence candidates were analyzed in vivo for their ability to modify mutant Huntingtin-induced eye degeneration and brain aggregation. We have established useful models for the study of human HD using the fly, and through our RNAi screen, we have identified new modifiers of mutant human Huntingtin aggregation and aggregate formation in the brain. Newly identified modifiers including genes related to nuclear transport, nucleotide processes, and signaling, may be involved in polyglutamine aggregate formation and Huntington disease cascades