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12

From a brief survey of the literature, it seems Kawasaki and Taira have been largely vindicated by the community before and since their paper. The retraction was by Taira alone, Kawasaki refused to co-sign because he maintained the data were valid. From the retraction it seems the reason for the retraction was a lost lab book. Prior to the Kawasaki and ...


6

People often imprecisely say that type of regulation takes place on the order of many minutes to hours, and that may be as precise as you can get given the variable kinetics of any given pathway. Also, all genes in eukaryotes require general transcription factors, but basically all of them also require activators to act first to recruit the GTFs and ...


6

A clarification on introns and exons. While it is true that introns are not a part of the mRNA as March Ho said, they are essentially transcribed. This may seem trivial but it is important to note. So: Both introns and exons arise from the transcribed region Exons need not necessarily form the ORF (i.e. be translated to proteins) Regarding intronic ...


4

While Ankur's answer is correct, it must be noted that not all non-coding RNAs are introns. An intron must be excised from an mRNA, which therefore means that any non-coding RNA that is not part of an mRNA cannot be an intron. For example, rRNA and tRNA are all examples of non-coding RNAs that are not introns, since they are not part of mRNA. miRNA may ...


3

First you should decide whether you want to design an shRNA or use siRNAs. If you want to use shRNA you should look at the rules that "Mad Scientist" mentioned. You can insert mismatches but make sure not to disrupt the secondary structure. You can use RNAFold to verify. shRNA always has issues and you have to optimize your design, test it by realtime ...


3

If gene B makes a protein product, you can try designing a morpholino against the 5'-UTR of gene B. This can prevent translation initiation at the ribosome as the morpholino occludes mRNA entry into the ribosome. You can detect this by western blotting. If gene B makes some sort of regulator RNA, you will need to target expression of gene B at the DNA ...


3

How well is gene A annotated? Do you have the gene A sequence (after post-transcriptional modifications)? If you do, you can order it from a company like DNA2.0 and they will synthesize it for you for like $0.35/base. Then you can transform the cells with this plasmid and do a knockout of gene B by inserting some sequence at the ~200bases overlap. Also, I ...


2

There are many studies that have used RNAi against the plant parasite M. incognita. The fundamental idea is that RNAi is directed against one of the vital genes of this nematode. Since, RNAi causes downregulation of the target gene, the nematode dies (or becomes ineffective in infecting) because of the loss of function of these important genes. As you might ...


2

Small non-coding RNAs are NOT generally abbreviated as sRNA but as sncRNA, if anything. I say "if anything" because the "small" part is subjective and just a portmanteau descriptor. The straight answer to your question is as Forest has written: miRNAs are a specific type of small non-coding RNA, some of which appear to function in the regulation of gene ...


2

miRNA are one member of the small non-coding RNA family. "Small non-coding" is a pretty broad term that encompasses microRNA and short interfering RNA, among other regulatory RNA species. The key word is 'regulatory'; each type of small non-coding RNA works by binding complementary sequences to exert some sort of regulatory control over gene expression. ...


1

Yup - in a lot of cases the transcription of non-coding RNAs is from introns. Some of them are within genes (intragenic) and others are intergenic (between genes). In humans, a large number of both have been documented http://www.nature.com/ng/journal/v47/n3/full/ng.3192.html Coming to your question about why they are not transcribed - it again comes down ...


1

What they're doing is called two-step PCR. In step one, some gene-specific primers with tags amplify genomic DNA, but the product has adapter regions now added to each end. In the second step, you add primers that complement the tag/adapter region and have T7 promoter sequences at the ends. Your second product will have the adapter region, and the T7 ...


1

The question is little bit unclear: is in vitro or in vivo introduction in question? In vivo: As the nematode feeds on the plant during its parasitic phase, it consequently assures the introduction of dsRNA and/or siRNA molecules into the nematode’s digestive system. in vitro introduction etc -> The status of RNAi-based transgenic research in ...


1

The answer is in the slides you provided a link to. The key fact is that Craig & Andy did careful controls to show that it was the presence of dsRNA in both the sense control, and in the anti-sense experimental sample that was responsible for the RNAi-mediated knock-down. Actually, Ken Kemphues showed this earlier in a Nature paper (the control also ...



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