citeulike.org - Joost van Delft Chemical research in toxicology, Vol. 25, No. 4. (16 April 2012), pp. 838-849, doi:10.1021/tx2003799 Toxicological studies assessing the safety of compounds for humans frequently use in vitro systems to characterize toxic responses in combination with transcriptomic analyses. Thus far, changes have mostly been investigated at the #mRNA level. Recently, #microRNAs have attracted attention because they are powerful negative regulators of #mRNA levels and, thus, may be responsible for the modulation… show all text posted by friends: (1) 
@sysbio: Benzo[a]pyrene-induced changes in #microRNA-#mRNA networks.: Chemical research in toxicology, Vol. 25, No. 4. (1… http://t.co/d5pBINBtiS 18.06.2013 16.29.02 
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http://bit.ly/10v8cf8 #rnomics_bioinfo
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@razZ0r: [delicious] RBPDB - The #RNA Binding Protein DataBase http://t.co/oNpdYJ0QJ1 RBPDB is a collection of #RNA-binding proteins linked to a … 18.06.2013 14.41.41 posted by followers of the list: (0) http://bit.ly/10v8cf3 #rnomics_bioinfo
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@razZ0r: [delicious] Transterm - #mRNA sequences and cis-regulatory elements http://t.co/EW4oGMhwKF Transterm, a database providing access to mR… 18.06.2013 14.41.37 posted by followers of the list: (0) http://bit.ly/10v8e6y #rnomics_bioinfo
by Hada Wuriyanghan, Bryce W. Falk The potato/tomato psyllid, _Bactericera cockerelli_ (_B. cockerelli_), is an important plant pest and the vector of the phloem-limited bacterium _Candidatus_ Liberibacter psyllaurous (solanacearum), which is associated with the zebra chip disease of potatoes. Previously, we reported induction of #RNA interference effects in _B. cockerelli_ via _in vitro_-prepared ds#RNA/#siRNAs after intrathoracic injection, and after feeding of artificial diets containing these effector #RNAs. In order to deliver #RNAi effectors via plant hosts and to rapidly identify effective target sequences in plant-feeding _B. cockerelli_, here we developed a plant virus vector-based _in planta_ system for evaluating candidate sequences. We show that recombinant _Tobacco mosaic virus_ (TMV) containing _B. cockerelli_ sequences can efficiently infect and generate small interfering #RNAs in tomato (_Solanum lycopersicum_), tomatillo (_Physalis philadelphica_) and tobacco (_Nicotiana tabacum_) plants, and more importantly delivery of interfering sequences via TMV induces #RNAi effects, as measured by actin and V-ATPase #mRNA reductions, in _B. cockerelli_ feeding on these plants. #RNAi effects were primarily detected in the _B. cockerelli_ guts. In contrast to our results with TMV, recombinant _Potato virus X_ (PVX) and _Tobacco rattle virus_ (TRV) did not give robust infections in all plants and did not induce detectable #RNAi effects in _B. cockerelli_. The greatest #RNA interference effects were observed when _B. cockerelli_ nymphs were allowed to feed on leaf discs collected from inoculated or lower expanded leaves from corresponding TMV-infected plants. Tomatillo plants infected with recombinant TMV containing _B. cockerelli actin_ or _V-ATPase_ sequences also showed phenotypic effects resulting in decreased _B. cockerelli_ progeny production as compared to plants infected by recombinant TMV containing _GFP_. These results showed that #RNAi effects can be achieved in plants against the phloem feeder, _B. cockerelli_, and the TMV-plant system will provide a faster and more convenient method for screening of suitable #RNAi target sequences _in planta_. http://bit.ly/1bSS6vt #PLoS
Background: Influenza A viruses possess #RNA genomes that mutate frequently in response to immune pressures. The mutations in the hemagglutinin genes are particularly significant, as the hemagglutinin proteins mediate attachment and fusion to host cells, thereby influencing viral pathogenicity and species specificity. Large-scale influenza A genome sequencing efforts have been ongoing to understand past epidemics and pandemics and anticipate future outbreaks. Sequencing efforts thus far have generated nearly 9,000 distinct hemagglutinin amino acid sequences.Description: Comparative models for all publicly available influenza A hemagglutinin protein sequences (8,769 to date) were generated using the Rosetta modeling suite. The C-alpha root mean square deviations between a randomly chosen test set of models and their crystallographic templates were less than 2 A, suggesting that the modeling protocols yielded high-quality results. The models were compiled into an online resource, the Hemagglutinin Structure Prediction (HASP) server. The HASP server was designed as a scientific tool for researchers to visualize hemagglutinin protein sequences of interest in a three-dimensional context. With a built-in molecular viewer, hemagglutinin models can be compared side-by-side and navigated by a corresponding sequence alignment. The models and alignments can be downloaded for offline use and further analysis. Conclusions: The modeling protocols used in the HASP server scale well for large amounts of sequences and will keep pace with expanded sequencing efforts. The conservative approach to modeling and the intuitive search and visualization interfaces allow researchers to quickly analyze hemagglutinin sequences of interest in the context of the most highly related experimental structures, and allow them to directly compare hemagglutinin sequences to each other simultaneously in their two- and three-dimensional contexts. The models and methodology have shown utility in current research efforts and the ongoing aim of the HASP server is to continue to accelerate influenza A research and have a positive impact on global public health. http://bit.ly/10uKIXl #BMC
Background: Influenza A viruses possess #RNA genomes that mutate frequently in response to immune pressures. The mutations in the hemagglutinin genes are particularly significant, as the hemagglutinin proteins mediate attachment and fusion to host cells, thereby influencing viral pathogenicity and species specificity. Large-scale influenza A genome sequencing efforts have been ongoing to understand past epidemics and pandemics and anticipate future outbreaks. Sequencing efforts thus far have generated nearly 9,000 distinct hemagglutinin amino acid sequences.Description: Comparative models for all publicly available influenza A hemagglutinin protein sequences (8,769 to date) were generated using the Rosetta modeling suite. The C-alpha root mean square deviations between a randomly chosen test set of models and their crystallographic templates were less than 2 A, suggesting that the modeling protocols yielded high-quality results. The models were compiled into an online resource, the Hemagglutinin Structure Prediction (HASP) server. The HASP server was designed as a scientific tool for researchers to visualize hemagglutinin protein sequences of interest in a three-dimensional context. With a built-in molecular viewer, hemagglutinin models can be compared side-by-side and navigated by a corresponding sequence alignment. The models and alignments can be downloaded for offline use and further analysis. Conclusions: The modeling protocols used in the HASP server scale well for large amounts of sequences and will keep pace with expanded sequencing efforts. The conservative approach to modeling and the intuitive search and visualization interfaces allow researchers to quickly analyze hemagglutinin sequences of interest in the context of the most highly related experimental structures, and allow them to directly compare hemagglutinin sequences to each other simultaneously in their two- and three-dimensional contexts. The models and methodology have shown utility in current research efforts and the ongoing aim of the HASP server is to continue to accelerate influenza A research and have a positive impact on global public health. http://bit.ly/10uKIXl #BMC
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Background: Similarly to the legume-rhizobia symbiosis, the arbuscular mycorrhiza interaction is controlled by autoregulation representing a feedback inhibition involving the CLAVATA1-like receptor kinase NARK in shoots. However, little is known about signals and targets down-stream of NARK. To find NARK-related transcriptional changes in mycorrhizal soybean (Glycine max) plants, we analyzed wild-type and two nark mutant lines interacting with the arbuscular mycorrhiza fungus Rhizophagus irregularis. Results: Affymetrix GeneChip analysis of non-inoculated and partially inoculated plants in a split-root system identified genes with potential regulation by arbuscular mycorrhiza or NARK. Most transcriptional changes occur locally during arbuscular mycorrhiza symbiosis and independently of NARK. RT-qPCR analysis verified nine genes as NARK-dependently regulated. Most of them have lower expression in roots or shoots of wild type compared to nark mutants, including genes encoding the receptor kinase GmSIK1, proteins with putative function as ornithine acetyl transferase, and a DEAD box #RNA helicase. A predicted annexin named GmAnnx1a is differentially regulated by NARK and arbuscular mycorrhiza in distinct plant organs. Two putative CCAAT-binding transcription factor genes named GmNF-YA1a and GmNF-YA1b are down-regulated NARK-dependently in non-infected roots of mycorrhizal wild-type plants and functional gene analysis confirmed a positive role for these genes in the development of an arbuscular mycorrhiza symbiosis. Conclusions: Our results indicate GmNF-YA1a/b as positive regulators in arbuscular mycorrhiza establishment, whose expression is down-regulated by NARK in the autoregulated root tissue thereby diminishing subsequent infections. Genes regulated independently of arbuscular mycorrhization by NARK support an additional function of NARK in symbioses-independent mechanisms. http://bit.ly/10t6cUq #BMC
The complexity, function and applications of #RNA in circulation
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