Bio-Network: Chara... Laboratory News: Grant for researchers to d... Biology Questions and Answers. Fjossinet: rna-js 0.1 committed on bi... BioMedCentral: RT @silencejournal: Metage... BioTechniques: Hybrid RNA-DNA Virus Ident... Fabrice Leclerc: RT @GeneQuan: qPCR NEWS Ap... Fabrice Jossinet: rna-js 0.1 committed on bi... Bioline: #Analytica #Biotech Forum,... J03_PY: sRNA Workbench 2.3.2 Beta:... Hybrid RNA-DNA Virus Identified. Hybrid RNA-DNA Virus Identified Diana Gitig, Ph.D. While doing fieldwork at Boiling Springs Lake in California, researchers have found a rather unusual genome, the result of recombination between DNA and RNA viruses.
Viruses mutate and trade genes all the time, which serves them really well but has not been so great for us. In addition to making it that much trickier for our immune systems to combat them, it has also made it much more difficult to study their evolution and to categorize them taxonomically. As we continue to figure them out, researchers at Portland State University in Oregon have discovered a completely new class of virus: an RNA-DNA hybrid virus. While doing fieldwork at Boiling Springs Lake in California, researchers have found a rather unusual genome, the result of recombination between DNA and RNA viruses. Source: Russell Virgilio, National Park Service References Diemer, G.S. and K.M. Invitrogen: Researchers discover natur... Hot spring yields hybrid genome. In the hostile environment of a bubbling volcanic hot spring, a team of researchers at Portland State University in Oregon has discovered a new viral genome that seems to be the product of recombination between a DNA virus and an RNA virus — a natural chimaera not seen before.
Their findings appeared on 19 April in the journal Biology Direct. “It’s a mythological beast of a virus, but it actually exists,” says virologist Ken Stedman, who coauthored the study. Image via Wikipedia under Creative Commons Boiling Springs Lake is home to a bizarre DNA-RNA hybrid virus. In the bacterial communities that populate the acidic waters of Boiling Springs Lake in northern California’s Lassen Volcanic National Park, “viruses are the only predators”, Stedman says. The resultant single-stranded circular genome, dubbed BSL RDHV (short for Boiling Springs Lake RNA–DNA hybrid virus), seems to be the result of a recombination event between two completely unrelated virus groups. Michael W. Pfaffl: qPCR NEWS April 2012 with...
Fjossinet: In rna-js, cmsearch and bl... Endre Sebestyén: scifi idea: real time meas... San Jose BioCenter: Firefly Bioworks: MicroRNA... Daniel MacArthur: Writing a review briefly m... Nutrigenomics: Remarkable findings of ing... Khader Shameer: C: A: Predict potential mi... Khader Shameer: A: Building a webpage for... Idtdna: Retracing your steps with... LifeTechSupport: Training Course: PGM™ RNA...
Bio_Network: Eleva... ASBMB: Podcast: “Caenorhabditis e... ASBMB: "The investigators conclud... Genome-wide Screen for miRNA Targets Using the MISSION Target ID Library. The Target ID Library is a plasmid-based, genome-wide collection of cloned cDNA used to identify miRNA targets. Here we demonstrate its use and application. Date Published: 4/06/2012, Issue 62; doi: 10.3791/3303 Keywords: Genetics, Issue 62, Target ID, miRNA, ncRNA, RNAi, genomics Cite this Article Coussens, M.
J., Forbes, K., Kreader, C., Sago, J., Cupp, C., Swarthout, J. The Target ID Library is designed to assist in discovery and identification of microRNA (miRNA) targets. To ensure broad coverage of the human transcriptome, Target ID Library cDNAs were generated via oligo-dT priming using a pool of total RNA prepared from multiple human tissues and cell lines Resulting cDNA range from 0.5 to 4 kb, with an average size of 1.2 kb, and were cloned into the p3΄TKzeo dual-selection plasmid (see Figure 4 for plasmid map). 1. 1.
Zeocin is used to select for stably transfected cells. Plate 1.6 x 104 cells into wells of a 96-well plate in 120 μl of media. 2. 2. 3. 3. 5. 6. 4. Figure 1. Chromatin Isolation by RNA Purification (ChIRP) ChIRP is a novel and rapid technique to map genomic binding sites of long noncoding RNAs (lncRNAs). The method takes advantage of the specificity of anti-sense tiling oligonucleotides to allow the enumeration of lncRNA-bound genomic sites. Date Published: 3/25/2012, Issue 61; doi: 10.3791/3912 Keywords: Genetics, Issue 61, long noncoding RNA (lncRNA), genomics, chromatin binding, high-throughput sequencing, ChIRP Cite this Article Chu, C., Quinn, J., Chang, H. Y. Long noncoding RNAs are key regulators of chromatin states for important biological processes such as dosage compensation, imprinting, and developmental gene expression 1,2,3,4,5,6,7.
Prior studies mapping RNA occupancy at chromatin have revealed substantial insights 15,16, but only at a single gene locus at a time. 1. Design anti-sense DNA tiling probes for selective retrieval of RNA target by ChIRP. Design anti-sense oligo probes using the online probe designer at singlemoleculefish.com 18. 2. 3. 4. 5. 6. 7. 8. 10. Figure 1. In vitro Transcription and Capping of Gaussia Luciferase mRNA Followed by HeLa Cell Transfection. This method describes high yield in vitro synthesis of both capped and uncapped mRNA from a linearized plasmid containing the Gaussia luciferase (GLuc) gene.
The RNA is purified and a fraction of the uncapped RNA is enzymatically capped using the Vaccinia virus capping enzyme. In the final step, the mRNA is transfected into HeLa cells and cell culture supernatants are assayed for luciferase activity. Date Published: 3/26/2012, Issue 61; doi: 10.3791/3702 Keywords: Genetics, Issue 61, In vitro transcription, Vaccinia capping enzyme, transfection, T7 RNA Polymerase, RNA synthesis Jani, B., Fuchs, R. In vitro Transcription and Capping of Gaussia Luciferase mRNA Followed by HeLa Cell Transfection. J. In vitro transcription is the synthesis of RNA transcripts by RNA polymerase from a linear DNA template containing the corresponding promoter sequence (T7, T3, SP6) and the gene to be transcribed (Figure 1A).
Large amounts of high quality RNA are often required for a variety of applications. 1. Shrikant Mantri: Hot Spring Yields New Hybr... GENbio: RT @illumina: Learn how RN... Bio_Network: Accur... Twitter. Bio_Network: Therm... Nature News&Comment: RT @m_m_campbell: Silence... Genome Biology: Global analysis of mRNA de... Bio-Network: Deep... View All. RNA Journal: "The ubiquitous hammerhead... Jason H. Moore, Ph.D: #genomics #genetics the wi... Agilent Life Science: 2 New NGS Webinars: #RNA C...
Michael W. Pfaffl: qPCR NEWS - Join our month... qPCR NEWS - monthly appearing qPCR newsletter. The ubiquitous hammerhead ribozyme. + Author Affiliations + Author Notes ↵5 Present address: Ribogenetics@Biochemistry Laboratory, Jacobs University Bremen, 28759 Bremen, Germany. Abstract The hammerhead ribozyme is a small catalytic RNA motif capable of endonucleolytic (self-) cleavage. It is composed of a catalytic core of conserved nucleotides flanked by three helices, two of which form essential tertiary interactions for fast self-scission under physiological conditions. Copyright © 2012 RNA Society. Michael W. Pfaffl: Modification of mRNA expre...
C&EN : #Photo of the Day: Six mim... MicrobeWorld: RNA studies under fire: Hi... Ruby Gadelrab: RNA-Seq studies under fire... Daniel MacArthur: Another excellent piece by... RNA Journal: "LocARNA-P: Accurate bound... 3D RNA modeling opens scientific doors. Monday, April 16, 2012 RNA hairpin Credit: Vossman/CC3.0 In a paper published today in the journal Nature Methods, a team from the University of North Carolina at Chapel Hill demonstrates a simple, cost-effective technique for three-dimensional RNA structure prediction that will help scientists understand the structures, and ultimately the functions, of the RNA molecules that dictate almost every aspect of human cell behavior.
When cell behavior goes wrong, diseases – including cancer and metabolic disorders – can be the result. Over the past five decades, scientists have described more than 80,000 protein structures, most of which are now publicly available and provide important information to medical researchers searching for targets for drug therapy. However, a similar effort to catalogue RNA structures has mapped only a few hundred RNA molecules. As a result, the potential of RNA molecules has just barely been developed as targets for new therapeutics.
"With Dr. Digitalbio: Eisen: metagenomic phyloty... Chris Gunter: See: as I mentioned last w... Nature News&Comment: RNA studies under fire htt... NatureNews: RNA studies under fire htt... RNA studies under fire. High-throughput RNA sequencing has yielded some unexpected results in the past few years — including some that seem to rewrite conventional wisdom in genetics. But a few of those findings are now being challenged, as computational biologists warn of the statistical pitfalls that can lurk in data-intensive studies. The latest case centres on imprinted genes. Humans and most other animals inherit two copies of most genes, one from each parent. But in some cases, only one copy is expressed; the other copy is silenced. In such cases, the gene is described as being imprinted.
In July 2010, a team led by Catherine Dulac and Christopher Gregg, both then at Harvard University in Cambridge, Massachusetts, published a study1 in Science estimating that 1,300 mouse genes — an order of magnitude more than previously known — were imprinted. Now, researchers are arguing that a flawed analysis led Dulac and Gregg to vastly overestimate imprinting in their paper. The Scientist: Remarkable findings of ing... Brian Krueger, PhD: 3D RNA modeling opens scie... Emblebi: RT @ewanbirney: Yummy new... BioTechniques: Effective DNA/RNA Co-Extra... ASBMB: Podcast: “Caenorhabditis e... ASBMB: "The investigators conclud... OpenHelix Staff: KUDOS! a pet peeve, many d... Agilent Life Science: A more complete characteri... Dgmacarthur: More hard evidence against... Dgmacarthur: Lesson: lots of false posi...
Daniel MacArthur: More hard evidence against... Daniel MacArthur: Lesson: lots of false posi... GENbio: Use of #siRNA in Therapeut... Use of siRNA in Therapeutic Arena on the Upswing. In contrast to miRNAs, siRNAs are usually perfectly complementary to their targets. They are thus very effective at eliminating gene expression. For this reason, synthetic siRNAs have been generated for a number of therapeutic uses.
But of course, there are hurdles: stability, potency, off-target effects, and efficient delivery of synthetic siRNAs are some of the major challenges for successful application of this technology in the clinic. Quark Pharmaceuticals is committed exclusively to developing siRNA drugs. One of its siRNAs has finished Phase II trials for the treatment of wet age-related macular degeneration and diabetic macular edema. This siRNA was licensed to Pfizer, which conducted the trials. Elena Feinstein, M.D., Ph.D., Quark’s CSO, spoke about some exciting results with another of the firm’s therapeutic siRNAs, this one to treat nonarteritic ischemic optic neuropathy, at Keystone Symposium’s recent “Nucleic Acid Therapeutics” conference.
Dr. MicrobeWorld: RNA virus packaging specif... Fabrice Jossinet: "Cooperative Tertiary Inte... MyBioTechniques: Hybrid RNA-DNA Virus Disco... Genome Biology: David Adams & @sangerinsti... Shrikant Mantri: Hot spring yields hybrid g... ASBMB: Come hear Elisabetta Ullu... ASBMB: The "team showed that the... Agilent Life Science: Join Us For Our Upcoming W... Biology Questions: Biology Questions and Answ... BioTechniques Daily Newsletter - Microscopy > Multi-Label Techniques for Colocalization StudieS User protocol for multi-color immunohistochemistry staining in intact tissue Double-staining and even triple-staining with poly- or monoclonal antibodies in immunohistochemistry (IHC) can enhance the study of colocalization—the presence of two or more antigens in one cell. Conventional methods for imaging colocalization, however, are prohibitive because overlapping colors are often indiscernible.
These generally applicable IHC staining methods can be widely applied in the biological sciences. CRi’s Nuance™ multispectral imaging system allows separation and subsequent quantitation of each antigen, including the counterstain, as well as autofluorescence removal in immunofluorescence (IF). Next-generation sequencing Power Next-Generation Sequencing with Innovative Sample Preparation Solutions from NuGEN®